Computer analysis and structure prediction of nucleic acids and proteins. - Minoru Kanehisa; P. Klein; P. Greif; Charles DeLisi (Nucleic Acids Res., 1984)

Loop closure via bond scaling and relaxation. - Qiang Zheng; Rakefet Rosenfeld; Sandor Vajda; Charles DeLisi (J. Comput. Chem., 1993)

Peptide docking using dynamic programming. - Kamalakar Gulukota; Sandor Vajda; Charles DeLisi (J. Comput. Chem., 1996)

Computational problems in cell biology. - Charles DeLisi; Sandor Vajda (Comput. Sci. Eng., 1999)

A hypothesis driven approach to condition specific transcription factor binding site characterization in S.c.. - Rhonda Harrison; Charles DeLisi (SAC, 2002)

Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. - Rhonda Harrison; Charles DeLisi (Bioinform., 2002)

Predictome: a database of putative functional links between proteins. - Joseph C. Mellor; Itai Yanai; Karl H. Clodfelter; Julian Mintseris; Charles DeLisi (Nucleic Acids Res., 2002)

Identification of functional links between genes using phylogenetic profiles. - Jie Wu 011; Simon Kasif; Charles DeLisi (Bioinform., 2003)

ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations. - Boris E. Shakhnovich; John M. Harvey; Steve Comeau; David Lorenz; Charles DeLisi; Eugene I. Shakhnovich (BMC Bioinform., 2003)

VisANT: an online visualization and analysis tool for biological interaction data. - Zhenjun Hu; Joseph C. Mellor; Jie Wu 011; Charles DeLisi (BMC Bioinform., 2004)

Discovery and Annotation of Genetic Modules. - Charles DeLisi (RECOMB, 2005)

VisANT: data-integrating visual framework for biological networks and modules. - Zhenjun Hu; Joe Mellor; Jie Wu 011; Takuji Yamada; Dustin T. Holloway; Charles DeLisi (Nucleic Acids Res., 2005)

An equilibrium partitioning model connecting gene expression and cis-motif content. - Joe Mellor; Charles DeLisi (ISMB (Supplement of Bioinformatics), 2006)

Comparative assessment of performance and genome dependence among phylogenetic profiling methods. - Evan S. Snitkin; Adam M. Gustafson; Joseph C. Mellor; Jie Wu 011; Charles DeLisi (BMC Bioinform., 2006)

Gene annotation and network inference by phylogenetic profiling. - Jie Wu 011; Zhenjun Hu; Charles DeLisi (BMC Bioinform., 2006)

Machine learning methods for transcription data integration. - Dustin T. Holloway; Mark A. Kon; Charles DeLisi (IBM J. Res. Dev., 2006)

SVMotif: A Machine Learning Motif Algorithm. - Mark A. Kon; Yue Fan; Dustin T. Holloway; Charles DeLisi (ICMLA, 2007)

Learning Methods for DNA Binding in Computational Biology. - Mark A. Kon; Dustin T. Holloway; Yue Fan; Chaitanya Sai; Charles DeLisi (IJCNN, 2007)

Portraits of breast cancer progression. - Gul S. Dalgin; Gabriela Alexe; Daniel Scanfeld; Pablo Tamayo; Jill P. Mesirov; Shridar Ganesan; Charles DeLisi; Gyan Bhanot (BMC Bioinform., 2007)

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. - Zhenjun Hu; David M. Ng; Takuji Yamada; Chunnuan Chen; Shuichi Kawashima; Joe Mellor; Bolan Linghu; Minoru Kanehisa; Joshua M. Stuart; Charles DeLisi (Nucleic Acids Res., 2007)

Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites. - Timothy E. Reddy; Charles DeLisi; Boris E. Shakhnovich (PLoS Comput. Biol., 2007)

Ensemble Machine Methods for DNA Binding. - Yue Fan; Mark A. Kon; Charles DeLisi (ICMLA, 2008)

VisANT: an integrative framework for networks in systems biology. - Zhenjun Hu; Evan S. Snitkin; Charles DeLisi (Briefings Bioinform., 2008)

High-precision high-coverage functional inference from integrated data sources. - Bolan Linghu; Evan S. Snitkin; Dustin T. Holloway; Adam M. Gustafson; Yu Xia 002; Charles DeLisi (BMC Bioinform., 2008)

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. - Zhenjun Hu; Jui-Hung Hung; Yan Wang; Yi-Chien Chang; Chia-Ling Huang; Matt Huyck; Charles DeLisi (Nucleic Acids Res., 2009)

Smoothing Gene Expression Using Biological Networks. - Yue Fan; Mark A. Kon; Shinuk Kim; Charles DeLisi (ICMLA, 2010)

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. - Richard J. Roberts; Yi-Chien Chang; Zhenjun Hu; John Rachlin; Brian P. Anton; Revonda M. Pokrzywa; Han-Pil Choi; Lina L. Faller; Jyotsna Guleria; Genevieve Housman; Niels Klitgord; Varun Mazumdar; et al. (Nucleic Acids Res., 2011)

Gene set enrichment analysis: performance evaluation and usage guidelines. - Jui-Hung Hung; Tun-Hsiang Yang; Zhenjun Hu; Zhiping Weng; Charles DeLisi (Briefings Bioinform., 2012)

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. - Chia-Ling Huang; John Lamb; Leonid Chindelevitch; Jarek Kostrowicki; Justin Guinney; Charles DeLisi; Daniel Ziemek (BMC Bioinform., 2012)

The NIH National Center for Integrative Biomedical Informatics (NCIBI). - Brian D. Athey; James D. Cavalcoli; H. V. Jagadish; Gilbert S. Omenn; Barbara Mirel; Matthias Kretzler; Charles F. Burant; Raphael D. Isokpehi; Charles DeLisi (J. Am. Medical Informatics Assoc., 2012)

Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer. - Daichi Shigemizu; Zhenjun Hu; Jui-Hung Hung; Chia-Ling Huang; Yajie Wang; Charles DeLisi (PLoS Comput. Biol., 2012)

VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. - Zhenjun Hu; Yi-Chien Chang; Yan Wang; Chia-Ling Huang; Yang Liu; Feng Tian; Brian Granger; Charles DeLisi (Nucleic Acids Res., 2013)

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. - Brian Granger; Yi-Chien Chang; Yan Wang; Charles DeLisi; Daniel Segrè; Zhenjun Hu (PLoS Comput. Biol., 2016)

The Mysterious Commonplace - A Life in Science - Charles DeLisi (The Mysterious Commonplace, 2021)