The inclusion of electrostatic hydration energies in molecular mechanics calculations. - Michael K. Gilson; Barry Honig (J. Comput. Aided Mol. Des., 1991)

A Fast Multipole Boundary Element Method for Molecular Electrostatics: An Optimal Approach for Large Systems. - Ranganathan Bharadwaj; Andreas Windemuth; S. Sriharan; Barry Honig; Antony Nocholls (J. Comput. Chem., 1995)

Bioinformatics in structural genomics - Editorial. - Burkhard Rost; Barry Honig; Alfonso Valencia (Bioinform., 2002)

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. - Walter Rocchia; Sundaram Sridharan; Anthony Nicholls; Emil Alexov; Alessandro Chiabrera; Barry Honig (J. Comput. Chem., 2002)

Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors. - Alona Sosinsky; Christopher P. Bonin; Richard S. Mann; Barry Honig (Nucleic Acids Res., 2003)

VISTAL - a new 2D visualization tool of protein 3D structural alignments. - Rachel Kolodny; Barry Honig (Bioinform., 2006)

PUDGE: a flexible, interactive server for protein structure prediction. - Raquel Norel; Donald Petrey; Barry Honig (Nucleic Acids Res., 2010)

VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity. - Brian Y. Chen; Barry Honig (PLoS Comput. Biol., 2010)

MarkUs: a server to navigate sequence-structure-function space. - Markus Fischer; Qiangfeng Cliff Zhang; Fabian Dey; Brian Y. Chen; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

PredUs: a web server for predicting protein interfaces using structural neighbors. - Qiangfeng Cliff Zhang; Lei Deng 002; Markus Fisher; Jihong Guan; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

Using Structure to Explore the Sequence Alignment Space of Remote Homologs. - Andrew Kuziemko; Barry Honig; Donald Petrey (PLoS Comput. Biol., 2011)

Using systems and structure biology tools to dissect cellular phenotypes. - Aris Floratos; Barry Honig; Dana Pe'er; Andrea Califano (J. Am. Medical Informatics Assoc., 2012)

PrePPI: a structure-informed database of protein-protein interactions. - Qiangfeng Cliff Zhang; Donald Petrey; José Ignacio Garzón; Lei Deng 002; Barry Honig (Nucleic Acids Res., 2013)

OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. - Shula Shazman; Hunjoong Lee; Yakov Socol; Richard S. Mann; Barry Honig (Nucleic Acids Res., 2014)

Predicting Peptide-Mediated Interactions on a Genome-Wide Scale. - T. Scott Chen; Donald Petrey; José Ignacio Garzón; Barry Honig (PLoS Comput. Biol., 2015)

miRNA-Disease Association Prediction with Collaborative Matrix Factorization. - Zhen Shen; You-Hua Zhang; Kyungsook Han; Asoke K. Nandi; Barry Honig; De-Shuang Huang (Complex., 2017)

Mutli-Features Prediction of Protein Translational Modification Sites. - Wenzheng Bao; Chang-An Yuan 001; Youhua Zhang; Kyungsook Han; Asoke K. Nandi; Barry Honig; De-Shuang Huang (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Integration of Multi-Omics Data for Gene Regulatory Network Inference and Application to Breast Cancer. - Lin Yuan 001; Lehang Guo; Chang-an Yuan 001; Youhua Zhang; Kyungsook Han; Asoke K. Nandi; Barry Honig; De-Shuang Huang (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)