Users Guide for SnadiOpt: A Package Adding Automatic Differentiation to Snopt - E. Michael Gertz; Philip E. Gill; Julia Muetherig (CoRR, 2001)

Object-oriented software for quadratic programming. - E. Michael Gertz; Stephen J. Wright 001 (ACM Trans. Math. Softw., 2003)

A starting point strategy for nonlinear interior methods. - E. Michael Gertz; Jorge Nocedal; Annick Sartenaer (Appl. Math. Lett., 2004)

A quasi-Newton trust-region method. - E. Michael Gertz (Math. Program., 2004)

A primal-dual trust region algorithm for nonlinear optimization. - E. Michael Gertz; Philip E. Gill (Math. Program., 2004)

WindowMasker: window-based masker for sequenced genomes. - Aleksandr Morgulis; E. Michael Gertz; Alejandro A. Schäffer; Richa Agarwala (Bioinform., 2006)

A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. - Aleksandr Morgulis; E. Michael Gertz; Alejandro A. Schäffer; Richa Agarwala (J. Comput. Biol., 2006)

The effectiveness of position- and composition-specific gap costs for protein similarity searches. - Aleksandar Stojmirovic; E. Michael Gertz; Stephen F. Altschul; Yi-Kuo Yu (ISMB, 2008)

Using an iterative linear solver in an interior-point method for generating support vector machines. - E. Michael Gertz; Joshua D. Griffin (Comput. Optim. Appl., 2010)

PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD. - Edward Michael Gertz; Tero Hiekkalinna; Sébastien Le Digabel; Charles Audet; Joseph D. Terwilliger; Alejandro A. Schäffer (BMC Bioinform., 2014)

Inferring models of multiscale copy number evolution for single-tumor phylogenetics. - Salim Akhter Chowdhury; E. Michael Gertz; Darawalee Wangsa; Kerstin Heselmeyer-Haddad; Thomas Ried; Alejandro A. Schäffer; Russell Schwartz (Bioinform., 2015)

Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data. - Haoyun Lei; Bochuan Lyu; E. Michael Gertz; Alejandro A. Schäffer; Russell Schwartz (ICCABS, 2018)

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. - Erfan Sadeqi Azer; Farid Rashidi Mehrabadi; Salem Malikic; Xuan Cindy Li; Osnat Bartok; Kevin Litchfield; Ronen Levy; Yardena Samuels; Alejandro A. Schäffer; E. Michael Gertz; Chi-Ping Day; Eva Pérez-Guijarro; et al. (Bioinform., 2020)

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. - Haoyun Lei; Bochuan Lyu; E. Michael Gertz; Alejandro A. Schäffer; Xulian Shi; Kui Wu 005; Guibo Li; Liqin Xu; Yong Hou; Michael Dean; Russell Schwartz (J. Comput. Biol., 2020)

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. - Haoyun Lei; E. Michael Gertz; Alejandro A. Schäffer; Xuecong Fu; Yifeng Tao; Kerstin Heselmeyer-Haddad; Irianna Torres; Guibo Li; Liqin Xu; Yong Hou; Kui Wu 005; Xulian Shi; et al. (Bioinform., 2021)