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Journal Articles
- 2019
[j18]Lin Yuan
, Lehang Guo, Chang-an Yuan, Youhua Zhang, Kyungsook Han, Asoke K. Nandi, Barry Honig, De-Shuang Huang:
Integration of Multi-Omics Data for Gene Regulatory Network Inference and Application to Breast Cancer. IEEE ACM Trans. Comput. Biol. Bioinform. 16(3): 782-791 (2019)- 2018
- [j17]Wenzheng Bao, Chang-An Yuan, Youhua Zhang, Kyungsook Han, Asoke K. Nandi, Barry Honig, De-Shuang Huang:
Mutli-Features Prediction of Protein Translational Modification Sites. IEEE ACM Trans. Comput. Biol. Bioinform. 15(5): 1453-1460 (2018) - 2017
- [j16]Zhen Shen, You-Hua Zhang, Kyungsook Han, Asoke K. Nandi, Barry Honig, De-Shuang Huang:
miRNA-Disease Association Prediction with Collaborative Matrix Factorization. Complex. 2017: 2498957:1-2498957:9 (2017) - 2015
- [j15]T. Scott Chen, Donald Petrey, José Ignacio Garzón, Barry Honig:
Predicting Peptide-Mediated Interactions on a Genome-Wide Scale. PLoS Comput. Biol. 11(5) (2015) - 2014
- [j14]Shula Shazman, Hunjoong Lee, Yakov Socol, Richard S. Mann, Barry Honig:
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res. 42(Database-Issue): 167-171 (2014) - 2013
- [j13]Qiangfeng Cliff Zhang, Donald Petrey, José Ignacio Garzón, Lei Deng, Barry Honig:
PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res. 41(Database-Issue): 828-833 (2013) - 2012
- [j12]Aris Floratos, Barry Honig, Dana Pe'er, Andrea Califano:
Using systems and structure biology tools to dissect cellular phenotypes. J. Am. Medical Informatics Assoc. 19(2): 171-175 (2012) - 2011
- [j11]Qiangfeng Cliff Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, Donald Petrey:
PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. 39(Web-Server-Issue): 283-287 (2011) - [j10]Markus Fischer, Qiangfeng Cliff Zhang, Fabian Dey, Brian Y. Chen, Barry Honig, Donald Petrey:
MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Res. 39(Web-Server-Issue): 357-361 (2011) - [j9]Andrew Kuziemko, Barry Honig, Donald Petrey:
Using Structure to Explore the Sequence Alignment Space of Remote Homologs. PLoS Comput. Biol. 7(10) (2011) - 2010
- [j8]Raquel Norel, Donald Petrey, Barry Honig:
PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Res. 38(Web-Server-Issue): 550-554 (2010) - [j7]Brian Y. Chen, Barry Honig:
VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity. PLoS Comput. Biol. 6(8) (2010) - 2006
- [j6]Rachel Kolodny, Barry Honig:
VISTAL - a new 2D visualization tool of protein 3D structural alignments. Bioinform. 22(17): 2166-2167 (2006) - 2003
- [j5]Alona Sosinsky, Christopher P. Bonin, Richard S. Mann, Barry Honig:
Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res. 31(13): 3589-3592 (2003) - 2002
- [j4]Burkhard Rost, Barry Honig, Alfonso Valencia:
Bioinformatics in structural genomics - Editorial. Bioinform. 18(7): 897 (2002) - [j3]Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig:
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. J. Comput. Chem. 23(1): 128-137 (2002) - 1995
- [j2]Ranganathan Bharadwaj, Andreas Windemuth, S. Sriharan, Barry Honig, Antony Nocholls:
A Fast Multipole Boundary Element Method for Molecular Electrostatics: An Optimal Approach for Large Systems. J. Comput. Chem. 16(7): 898-913 (1995) - 1991
- [j1]Michael K. Gilson, Barry Honig:
The inclusion of electrostatic hydration energies in molecular mechanics calculations. J. Comput. Aided Mol. Des. 5(1): 5-20 (1991)
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