Theoretical Aspects of the Complex: Arts and New Technologies. - Dimitris K. Agrafiotis (IFIP Congress (2), 1994)

On the Use of Information Theory for Assessing Molecular Diversity. - Dimitris K. Agrafiotis (J. Chem. Inf. Comput. Sci., 1997)

Stochastic Algorithms for Maximizing Molecular Diversity. - Dimitris K. Agrafiotis (J. Chem. Inf. Comput. Sci., 1997)

An Efficient Implementation of Distance-Based Diversity Measures Based on k-d Trees. - Dimitris K. Agrafiotis; Victor S. Lobanov (J. Chem. Inf. Comput. Sci., 1999)

Ultrafast Algorithm for Designing Focused Combinational Arrays. - Dimitris K. Agrafiotis; Victor S. Lobanov (J. Chem. Inf. Comput. Sci., 2000)

Nonlinear Mapping Networks. - Dimitris K. Agrafiotis; Victor S. Lobanov (J. Chem. Inf. Comput. Sci., 2000)

Stochastic Similarity Selections from Large Combinatorial Libraries. - Victor S. Lobanov; Dimitris K. Agrafiotis (J. Chem. Inf. Comput. Sci., 2000)

Multiobjective optimization of combinatorial libraries. - Dimitris K. Agrafiotis (IBM J. Res. Dev., 2001)

Multidimensional scaling of combinatorial libraries without explicit enumeration. - Dimitris K. Agrafiotis; Victor S. Lobanov (J. Comput. Chem., 2001)

Multidimensional scaling and visualization of large molecular similarity tables. - Dimitris K. Agrafiotis; Dmitrii N. Rassokhin; Victor S. Lobanov (J. Comput. Chem., 2001)

Nonlinear mapping of massive data sets by fuzzy clustering and neural networks. - Dmitrii N. Rassokhin; Victor S. Lobanov; Dimitris K. Agrafiotis (J. Comput. Chem., 2001)

A Constant Time Algorithm for Estimating the Diversity of Large Chemical Libraries. - Dimitris K. Agrafiotis (J. Chem. Inf. Comput. Sci., 2001)

Design and Prioritization of Plates for High-Throughput Screening. - Dimitris K. Agrafiotis; Dmitrii N. Rassokhin (J. Chem. Inf. Comput. Sci., 2001)

A Novel Method for Building Regression Tree Models for QSAR Based on Artificial Ant Colony Systems. - Sergei Izrailev; Dimitris K. Agrafiotis (J. Chem. Inf. Comput. Sci., 2001)

On the Use of Neural Network Ensembles in QSAR and QSPR. - Dimitris K. Agrafiotis; Walter Cedeño; Victor S. Lobanov (J. Chem. Inf. Comput. Sci., 2002)

A Fractal Approach for Selecting an Appropriate Bin Size for Cell-Based Diversity Estimation. - Dimitris K. Agrafiotis; Dmitrii N. Rassokhin (J. Chem. Inf. Comput. Sci., 2002)

A self-organizing principle for learning nonlinear manifolds. - Dimitris K. Agrafiotis; Huafeng Xu (Proc. Natl. Acad. Sci. USA, 2002)

Using particle swarms for the development of QSAR models based on K-nearest neighbor and kernel regression. - Walter Cedeño; Dimitris K. Agrafiotis (J. Comput. Aided Mol. Des., 2003)

Stochastic proximity embedding. - Dimitris K. Agrafiotis (J. Comput. Chem., 2003)

A Geodesic Framework for Analyzing Molecular Similarities. - Dimitris K. Agrafiotis; Huafeng Xu (J. Chem. Inf. Comput. Sci., 2003)

Nearest Neighbor Search in General Metric Spaces Using a Tree Data Structure with a Simple Heuristic. - Huafeng Xu; Dimitris K. Agrafiotis (J. Chem. Inf. Comput. Sci., 2003)

Conformational Sampling by Self-Organization. - Huafeng Xu; Sergei Izrailev; Dimitris K. Agrafiotis (J. Chem. Inf. Comput. Sci., 2003)

A Comparison of Particle Swarms Techniques for the Development of Quantitative Structure-Activity Relationship Models for Drug Design. - Walter Cedeño; Dimitris K. Agrafiotis (CSB Workshops, 2005)

A distance geometry heuristic for expanding the range of geometries sampled during conformational search. - Sergei Izrailev; Fangqiang Zhu; Dimitris K. Agrafiotis (J. Comput. Chem., 2006)

A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries and Its Application to a Recent Acquisition. - Michael F. M. Engels; Alan C. Gibbs; Edward P. Jaeger; Danny Verbinnen; Victor S. Lobanov; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2006)

Self-organizing superimposition algorithm for conformational sampling. - Fangqiang Zhu; Dimitris K. Agrafiotis (J. Comput. Chem., 2007)

Advanced Biological and Chemical Discovery (ABCD): Centralizing Discovery Knowledge in an Inherently Decentralized World. - Dimitris K. Agrafiotis; Simson Alex; Heng Dai; An Derkinderen; Michael Farnum; Peter Gates; Sergei Izrailev; Edward P. Jaeger; Paul Konstant; Albert Leung; Victor S. Lobanov; Patrick Marichal; et al. (J. Chem. Inf. Model., 2007)

Radial Clustergrams: Visualizing the Aggregate Properties of Hierarchical Clusters. - Dimitris K. Agrafiotis; Deepak Bandyopadhyay; Michael Farnum (J. Chem. Inf. Model., 2007)

Conformational Sampling of Bioactive Molecules: A Comparative Study. - Dimitris K. Agrafiotis; Alan C. Gibbs; Fangqiang Zhu; Sergei Izrailev; Eric J. Martin (J. Chem. Inf. Model., 2007)

Recursive Distance Partitioning Algorithm for Common Pharmacophore Identification. - Fangqiang Zhu; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2007)

A self-organizing algorithm for molecular alignment and pharmacophore development. - Deepak Bandyopadhyay; Dimitris K. Agrafiotis (J. Comput. Chem., 2008)

Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss. - Pascal Bonnet; Dimitris K. Agrafiotis; Fangqiang Zhu; Eric J. Martin (J. Chem. Inf. Model., 2009)

Enhanced SAR Maps: Expanding the Data Rendering Capabilities of a Popular Medicinal Chemistry Tool. - Jeremy Kolpak; Peter J. Connolly; Victor S. Lobanov; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2009)

Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use. - Gary Tresadern; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2009)

A Self-Organizing Algorithm for Modeling Protein Loops. - Pu Liu; Fangqiang Zhu; Dmitrii N. Rassokhin; Dimitris K. Agrafiotis (PLoS Comput. Biol., 2009)

Fast determination of the optimal rotational matrix for macromolecular superpositions. - Pu Liu; Dimitris K. Agrafiotis; Douglas L. Theobald (J. Comput. Chem., 2010)

Rapid communication reply to comment on: "Fast determination of the optimal rotational matrix for macromolecular superpositions". - Pu Liu; Dimitris K. Agrafiotis; Douglas L. Theobald (J. Comput. Chem., 2011)

Efficient Substructure Searching of Large Chemical Libraries: The ABCD Chemical Cartridge. - Dimitris K. Agrafiotis; Victor S. Lobanov; Maxim Shemanarev; Dmitrii N. Rassokhin; Sergei Izrailev; Edward P. Jaeger; Simson Alex; Michael Farnum (J. Chem. Inf. Model., 2011)

Single R-Group Polymorphisms (SRPs) and R-Cliffs: An Intuitive Framework for Analyzing and Visualizing Activity Cliffs in a Single Analog Series. - Dimitris K. Agrafiotis; John J. M. Wiener; Andrew Skalkin; Jeremy Kolpak (J. Chem. Inf. Model., 2011)

Library Enhancement through the Wisdom of Crowds. - Michael D. Hack; Dmitrii N. Rassokhin; Christophe Buyck; Mark Seierstad; Andrew Skalkin; Peter ten Holte; Todd K. Jones; Taraneh Mirzadegan; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2011)

Power Keys: A Novel Class of Topological Descriptors Based on Exhaustive Subgraph Enumeration and their Application in Substructure Searching. - Pu Liu; Dimitris K. Agrafiotis; Dmitrii N. Rassokhin (J. Chem. Inf. Model., 2011)

Accelerating Chemical Database Searching Using Graphics Processing Units. - Pu Liu; Dimitris K. Agrafiotis; Dmitrii N. Rassokhin; Eric Yang (J. Chem. Inf. Model., 2011)

Stochastic Proximity Embedding on Graphics Processing Units: Taking Multidimensional Scaling to a New Scale. - Eric Yang; Pu Liu; Dmitrii N. Rassokhin; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2011)

Clinical Case: Enhancing medical monitoring with visualization and analytics. - Michael Farnum; Victor S. Lobanov; Michael Brennan; Dimitris K. Agrafiotis; Jeremy Kolpak; Joseph Ciervo; Laurent Alquier (BIBM, 2012)

Recognizing Pitfalls in Virtual Screening: A Critical Review. - Thomas Scior; Andreas Bender 002; Gary Tresadern; José L. Medina-Franco; Karina Martínez-Mayorga; Thierry Langer; Karina Cuanalo-Contreras; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2012)

Stochastic Proximity Embedding: A Simple, Fast and Scalable Algorithm for Solving the Distance Geometry Problem. - Dimitris K. Agrafiotis; Deepak Bandyopadhyay; Eric Yang (Distance Geometry, 2013)

Chemistry, information and Frank: a tribute to Frank Brown. - Dimitris K. Agrafiotis; M. Katharine Holloway; Scott A. Johnson; Charles H. Reynolds; Terry R. Stouch; Alexander Tropsha; Chris L. Waller (J. Comput. Aided Mol. Des., 2018)

A cross-source, system-agnostic solution for clinical data review. - Michael Farnum; Mathangi Ashok; Daniel Kowalski; Fang Du; Lalit Mohanty; Paul Konstant; Joseph Ciervo; Victor S. Lobanov; Dimitris K. Agrafiotis (Database J. Biol. Databases Curation, 2019)

A dimensional warehouse for integrating operational data from clinical trials. - Michael Farnum; Lalit Mohanty; Mathangi Ashok; Paul Konstant; Joseph Ciervo; Victor S. Lobanov; Dimitris K. Agrafiotis (Database J. Biol. Databases Curation, 2019)

A late-binding, distributed, NoSQL warehouse for integrating patient data from clinical trials. - Eric Yang; Jeremy D. Scheff; Shih C. Shen; Michael Farnum; James Sefton; Victor S. Lobanov; Dimitris K. Agrafiotis (Database J. Biol. Databases Curation, 2019)

Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator. - Veerabahu Shanmugasundaram; Jürgen Bajorath; Ralph E. Christoffersen; James D. Petke; W. Jeffrey Howe; Mark A. Johnson; Dimitris K. Agrafiotis; Pil Lee; Leslie A. Kuhn; Jay T. Goodwin; M. Katharine Holloway; Thompson N. Doman; et al. (J. Comput. Aided Mol. Des., 2022)