Mining Residue Contacts in Proteins. - Mohammed Javeed Zaki; Shan Jin; Chris Bystroff (BIBE, 2000)

Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence. - Edward C. Thayer; Chris Bystroff; David Baker 001 (J. Comput. Biol., 2000)

Fully automated ab initio protein structure prediction using I-STES, HMMSTR and ROSETTA. - Chris Bystroff; Yu Shao (ISMB, 2002)

Mining Protein Contact Maps. - Jingjing Hu; Xiaolan Shen; Yu Shao; Chris Bystroff; Mohammed Javeed Zaki (BIOKDD, 2002)

Efficient remote homology detection using local structure. - Yuna Hou; Wynne Hsu; Mong-Li Lee; Chris Bystroff (Bioinform., 2003)

Mining residue contacts in proteins using local structure predictions. - Mohammed Javeed Zaki; Shan Jin; Chris Bystroff (IEEE Trans. Syst. Man Cybern. Part B, 2003)

Predicting protein folding pathways. - Mohammed Javeed Zaki; Vinay Nadimpally; Deb Bardhan; Chris Bystroff (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Predicting Protein Folding Pathways. - Mohammed Javeed Zaki; Vinay Nadimpally; Deb Bardhan; Chris Bystroff (Data Mining in Bioinformatics, 2005)

ECOME: A simple model for an evolving consumption web. - Christopher Bystroff; Sam DeLuca; Carl N. McDaniel (CSB Workshops, 2005)

Efficient Sampling of Protein Folding Pathways using HMMSTR and Efficient Sampling of Protein Folding Pathways using HMMSTR and. - Yogesh A. Girdhar; Christopher Bystroff; Srinivas Akella (CSB Workshops, 2005)

Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions. - Yao-ming Huang; Christopher Bystroff (CSB Workshops, 2005)

Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. - Xin Yuan; Christopher Bystroff (Bioinform., 2005)

Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. - Yao-ming Huang; Christopher Bystroff (Bioinform., 2006)

Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure. - Christopher Bystroff; Bobbie-Jo M. Webb-Robertson (BMC Bioinform., 2008)

Iterative Non-Sequential protein Structural Alignment. - Saeed Salem; Mohammed J. Zaki; Christopher Bystroff (J. Bioinform. Comput. Biol., 2009)

FlexSnap: Flexible Non-sequential Protein Structure Alignment. - Saeed Salem; Mohammed J. Zaki; Chris Bystroff (Algorithms Mol. Biol., 2010)

Exploring objective functions and cross-terms in the optimization of an energy function for protein design. - Yao-ming Huang; Christopher Bystroff (BCB, 2012)

Expanded Explorations into the Optimization of an Energy Function for Protein Design. - Yao-ming Huang; Chris Bystroff (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design. - Derek J. Pitman; Christian D. Schenkelberg; Yao-ming Huang; Frank D. Teets; Daniel J. DiTursi; Christopher Bystroff (Bioinform., 2014)

InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite. - Christian D. Schenkelberg; Christopher Bystroff (Bioinform., 2015)

Protein backbone ensemble generation explores the local structural space of unseen natural homologs. - Christian D. Schenkelberg; Christopher Bystroff (Bioinform., 2016)

Fast design of arbitrary length loops in proteins using InteractiveRosetta. - William F. Hooper; Benjamin D. Walcott; Xing Wang 009; Christopher Bystroff (BMC Bioinform., 2018)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

Challenges and Solutions for Leave-One-Out Biosensor Design in the Context of a Rugged Fitness Landscape. - Shounak Banerjee; Keith Fraser; Donna E. Crone; Jinal C. Patel; Sarah E. Bondos; Christopher Bystroff (Sensors, 2024)