|
Johnson
& Johnson Pharmaceutical Research & Development Personal E-mail: dimitris.agrafiotis@gmail.com |
|
Informatics
executive with extensive experience in building and leading large
multi-disciplinary informatics groups to support pharmaceutical R&D, in
both biotech and large pharma.
Experienced
global leader with proven ability to identify strategic initiatives, align
stakeholders, and deliver elegant and workable solutions on time and on budget.
Widely
published and respected scientist with extensive background in informatics and
modeling, structure-based drug design, medicinal and combinatorial chemistry,
high-throughput screening, biophysics, and translational technologies. Extensive public sector advisory work.
Accomplished
software architect and information integrator, creator of numerous highly
successful enterprise-wide information management systems used by thousands of
scientists around the world, including discovery data warehouses, electronic
lab notebooks, compound and sample management systems,
high-throughput/high-content screening platforms, and advanced data mining,
analysis and visualization tools to support discovery,
clinical, epidemiological, and translational research.
Entrepreneur and innovator with extensive
experience in intellectual property development. Inventor on 18
issued US patents in multiple areas of informatics and computational drug
design.
Advocate
of empowered leadership with a passion for building organizational frameworks
that promote collaboration, engagement and connectivity across functional,
regional, and cultural boundaries.
|
1990 - 1991 |
Harvard University |
|
1988 - 1990 |
University of California, Berkeley |
|
1985 - 1988 |
Ph.D., Imperial College of Science
& Technology, University of London |
|
1981 - 1985 |
B.S., University of Patras, Greece |
|
2003 - Pres. |
Johnson & Johnson
Pharmaceutical Research & Development, L.L.C. Johnson
& Johnson Pharmaceutical Research & Development, L.L.C. Indiana
University School of Informatics, Bloomington University of Athens School of Pharmacy |
|
1994 - 2003. |
3-Dimensional Pharmaceuticals, Inc. |
|
1991 - 1994 |
Parke-Davis Pharmaceutical
Research, Warner-Lambert Co. (now Pfizer Inc.) Development of new parallel biomolecular docking algorithms based on
simulated annealing and Darwinian evolution. Molecular modeling of growth
factors. Pharmacophore modeling of selected antibacterial quinolones.
Development of a large library of reusable software tools for molecular
modeling applications. |
|
1990 - 1991 |
Harvard University Enhancements to the LHASA program for computer-assisted synthetic
analysis. Development of a new suite of algorithms for the rapid three-dimensionalization of molecular structures, that allow
LHASA to determine the stability of compounds generated in the course of a
retrosynthetic analysis, to estimate equilibrium compositions and to
determine the stereochemical outcome of reactions
controlled by steric approach preferences . |
|
1988 - 1990 |
University of California, Berkeley Development of the electron density analysis program PRODEN. The
program computes projected, planar and three-dimensional densities from ab initio wave-functions, and calculates
atomic populations by demarkating and integrating
the two-dimensional data. Development of graphics routines for rendering
atomic virial surfaces and their PRODEN
approximations, and integration into a portable general-use graphics package.
Ab initio calculations on the
solvation effects on the structure and electronic structure of lithium amide dimer, the pseudorotation
mechanism of model phosphoranes, and the effects of
adjacent heteroatoms in carbanion
stability. |
|
1985 - 1988 |
Imperial College of Science &
Technology, University of London Theoretical SCF-MO investigation of the reaction mechanisms, substituent effects and kinetic isotope effects of dihydrogen transfers, dihydrogen eliminations, the Baeyer-Villiger and Stevens rearrangements and 2-azirine rearrangements, using semi-empirical and ab initio theory. Implementation and evaluation of the Broyden-Fletcher-Goldfarb-Shanno variable metric minimization algorithm for geometry optimization, using the MNDO and AM1 procedures. Development of a portable computer graphics package for contouring, surface rendering and molecular plotting. |
|
Chemoiformatics, bioinformatics, biomedical informatics, data
integration, data visualization, computational chemistry, computational
biology, computer-assisted drug design, artificial intelligence, algorithms,
software engineering. |
|
2009 |
Harvard Business School Johnson
& Johnson Strategic Leadership Program |
|
2008 |
The Wharton School, University of
Pennsylvania |
|
2001 |
Massachusetts Institute of
Technology |
|
1992 |
Drew University |
|
2003 |
Innovative Combinatorial
Approaches and Technologies |
|
1998 |
2nd European Workshop in Drug
Design |
|
1986 - 1988 |
Imperial College of Science &
Technology, University of London |
|
|
|
2007 - pres |
Editorial Board, Journal of
Chemical Information & Modeling |
|
1999 - pres |
Editorial Board, Molecular
Informatics |
|
2005 - 2009 |
Editorial Board, Journal of
Molecular Graphics & Modeling |
|
2005 - pres |
Editorial
Board, Chemical Biology & Drug Design |
|
2007 - pres |
Editorial Board, Molecular
Diversity |
|
2005 - pres |
Board of
Directors, International QSAR & Modeling Society (http://www.qsar.org/) |
|
2007 - pres |
Board of Trustees, Chemical
Structure Association Trust (http://www.csa-trust.org/) |
|
2005 - pres |
Scientific Advisory Board, NIH
Center for Chemoinformatics Research, Indiana University School of
Informatics |
|
2005 - pres |
Scientific Advisory Board, NIH
Center for Chemoinformatics Research, University of North Carolina at Chapel
Hill |
|
2006 - pres |
Scientific Advisory Board, NIH
Center for Chemoinformatics Research, Rensselaer Polytechnic Intitute |
|
2005 - pres |
NIH Review Committee, NIH Roadmap,
Computational Biophysics |
|
2003 |
Scientific Advisory Board, IBC
Conference on Design & Synthesis of Target Based Compound Libraries |
|
2000 |
Guest Editor, Special Issue on
Combinatorial Library Design, Journal of Molecular Graphics and Modeling |
|
2004 |
Scientific Advisory Board, EuroQSAR 2004 |
|
2005 |
Scientific Advisory Board &
Conference Organizer, Pacifichem 2005 |
|
2005 - 2011 |
Scientific Advisory Board,
International Conference on Chemical Structures (ICCS) |
|
2010 |
Co-Chair, EuroQSAR
2010 |
|
1996 - pres |
Reviewer |
|
1986 - 1988 |
Alexander Onassis Fellowship,
Imperial College of Science & Technology |
|
1988 - 1989 |
Alexander Onassis Fellowship,
University of California, Berkeley |
|
1999 |
Outstanding Achievement Award,
3-Dimensional Pharmaceuticals, Inc. |
|
2005 |
J&J Image Award (outstanding
application of information technology) |
American Chemical
Society
American Association for the Advancement of Science
Association
of Greek Chemists
|
Dr. Michael Jackson
Vice President, Drug Discovery & Development,
Sanford Burnham Medical Research Institute, La Jolla, CA
(Formerly Senior VP of Drug Discovery and Chief Scientific Officer at Johnson
& Johnson Pharmaceutical Research & Development)
Tel: +1 (858) 795-5201
E-mail: mjackson@sanfordburnham.org
Dr. F. Raymond Salemme
CEO at Redpoint Bio Corporation
(Formerly Founder, President and CSO of 3-Dimensional Pharmaceuticals, Inc.)
Tel: +1 (215) 504-0836
E-mail: fsalemme1@comcast.net
Dr. John Reynders
Vice President, Information, AstraZeneca
(Formerly Senior VP and Chief Information Officer at Johnson & Johnson
Pharmaceutical Research & Development)
Tel: +1 (781) 839-4915
E-mail: john.reynders@astrazeneca.com
Dr. David UPrichard
President, Druid Consulting, LLC
(Formerly Chairman of R&D at SmithKline Beecham, and CEO of 3-Dimensional
Pharmaceuticals, Inc.)
Tel: +1 (215) 928-9226
E-mail: dcuprichard@druidconsult.com
Prof. Elias J.
Corey
Department of Chemistry, Harvard University, Cambridge, MA
Tel: +1 (617) 495-4033
E-mail: corey@chemistry.harvard.edu
Prof. Michael Levitt
Chairman,
Department of Structural and Cell Biology, Stanford
University, Stanford, CA
Tel: +1 (415) 723-6800
E-mail: levitt@hyper.stanford.edu
1. Agrafiotis DK*. Molecular orbital
studies of dihydrogen transfers and other reactions. Ph.D. Thesis, Department of Chemistry, Imperial College of Science
& Technology, University of London, 1988.
2. Graybill TL*, Agrafiotis DK,
Bone R, Illig CR, Jaeger EP, Locke KT, Lu T, Salvino JM, Soll
RM, Spurlino JC, Subasinghe N, Tompczuk BE, Salemme
FR. Enhancing the drug discovery process by integration of high-throughput
chemistry and structure-based drug design. In Molecular Diversity and Combinatorial
Chemistry, Chaiken IM, Janda
KD, Eds., ACS, Washington D. C., 1996, 16-26.
3. Agrafiotis DK*. Diversity of
chemical libraries. In The Encyclopedia of
Computational Chemistry, Schleyer PvR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer
III HF, Schreiner PR, Eds., John Wiley and Sons, Chichester, 1998, Vol.
1, 742-761. [PDF]
4. Agrafiotis DK*, Myslik JP, Salemme FR. Advances in diversity profiling and
combinatorial series design. In Annual Reports in Combinatorial Chemistry
and Molecular Diversity, Pavia M, Moos W, Eds., Kluwer,
1999, 2, 71-92.
5. Agrafiotis DK*, Lobanov VS, Rassokhin DN, Izrailev S. The measurement of molecular diversity. In Virtual
Screening of Bioactive Molecules, Böhm H-J,
Schneider G, Eds., Wiley-VCH, Weinheim, 2000, 265-300.
6. Farnum M, DesJarlais
R, Agrafiotis DK*. Molecular diversity. In Chemoinformatics
- From Data to Knowledge, Gasteiger J, EEd., John Wiley & Sons, Chichester, 2003.
7. Gibbs AC, Agrafiotis DK*. Chemical diversity: definition and
quantification. In Exploiting Chemical Diversity for Drug Discovery,
Bartlett P, Entzeroth M, Eds., The Royal Society of
Chemistry, 2006, 139-160.
8. Krein M, Huang T-W,
Morkowchuk L, Agrafiotis DK; Breneman CM. Developing best practices for
descriptor-based property prediction: appropriate matching of datasets,
descriptors, methods, and expectations. In Statistical Modelling
of Molecular Descriptors in QSAR/QSPR. Dehmer M, Varmuza
K, Bonchev B, Eds,
Wiley-VCH, 2011, in press.
8. Agrafiotis DK, Rzepa HS*. Dihydrogen transfer reactions. An SCF-MO
study of the relative energies of the concerted and stepwise pathways. J.
Chem. Soc., Chem. Commun. 1987, 902.
9. Agrafiotis DK, Rzepa HS*. Evaluation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) variable metric method in geometry
optimisation using semi-empirical SCF-MO procedures. J. Chem. Research (S)
1988, 101.
10. Agrafiotis DK, Rzepa HS*. A theoretical MNDO and AM1 SCF-MO study of dihydrogen
elimination reactions. J. Chem. Soc., Perkin Trans. II 1989, 367.
11. Agrafiotis DK, Rzepa HS*. A theoretical MNDO and AM1 SCF-MO study of dihydrogen
transfer reactions. J. Chem. Soc.,
Perkin Trans. II 1989, 475.
12. Agrafiotis DK*, Streitwieser
A, Rzepa
HS, MOLECULE: A GKS graphical
display package. QCPE Bull. 1989, 9, 127, Program 583.
13. Wang P, Agrafiotis DK,
Streitwieser A*, Schleyer PvR*.
Berry and turnstyle processes in the preudorotation of three phosphoranes.
J. Chem. Soc., Chem. Commun. 1990, 201.
14. Agrafiotis DK, Tansy BL, Streitwieser A*. PRODEN, a new electron density analysis
program. J. Comp. Chem. 1990, 11(9), 1101.
15. Agrafiotis DK*, Tansy B, Streitwieser A. PRODEN: A new electron density analysis program. QCPE Bull. 1991, 11, 13, Program 600.
16. Spiegel K, Agrafiotis DK,
Carpathe B, Davis RE, Dickerson MR, Fergus JH,
Hepburn TW, Marks JS, Van Dorf M, Wieland DM, Jaen
JC*. PD 90780, a non-peptide inhibitor of nerve growth factors binding to the
P75 NGF receptor. Biochem. Biophys. Res. Comm. 1995, 217(2), 488.
17. Agrafiotis DK*. Stochastic
algorithms for maximizing molecular diversity. 3-rd Elec. Comput. Chem. Conf. 1996.
18. Agrafiotis DK*. A new method
for analyzing protein sequence relationships based on Sammon
maps. Protein Sci. 1997, 6(2), 287. [PDF]
19. Agrafiotis DK*. On the use of information
theory for assessing molecular diversity. J. Chem. Info. Comp. Sci. 1997,
37(3), 576. [PDF]
20. Agrafiotis DK*. Stochastic
algorithms for maximizing molecular diversity. J. Chem. Info. Comp. Sci. 1997,
37(5), 841.
[PDF]
21. Agrafiotis DK*, Myslik JP, Salemme FR. Advances in diversity profiling and
combinatorial series design. Mol. Diversity 1999, 4, 1-22.
[PDF]
22. Agrafiotis DK*, Lobanov VS.
An efficient implementation of distance-based diversity metrics based on k-d
trees. J. Chem. Info. Comp. Sci. 1999, 39(1), 51-58. [PDF]
23. Lobanov VS*, Agrafiotis DK.
Stochastic similarity selections from large combinatorial libraries. J.
Chem. Info. Comput. Sci. 2000, 40,
460-470. [PDF]
24. Agrafiotis DK*, Lobanov VS.
Ultrafast algorithm for designing focused combinatorial arrays. J. Chem.
Info. Comput. Sci. 2000, 40,
1030-1038. [PDF]
25. Boyd DB, Agrafiotis DK, Martin EJ.
Introduction and forward to the special issue on combinatorial library design. J.
Mol. Graphics Modell. 2000, 18,
317-319.
26. Rassokhin DN, Agrafiotis DK*. Kolmogorov-Smirnov
statistic and its applications in library design. J. Mol. Graphics Modell. 2000, 18(4-5), 370-384. [PDF]
27. Agrafiotis DK*, Lobanov VS.
Nonlinear mapping networks. J. Chem. Info. Comput.
Sci. 2000, 40, 1356-1362. [PDF]
28. Agrafiotis DK*. A constant
time algorithm for estimating the diversity of large chemical libraries. J.
Chem. Info. Comput. Sci. 2001, 41(1),
159-167 [PDF].
29. Izrailev S*, Agrafiotis DK.
A new method for building regression tree models for QSAR based on artificial
ant colony systems. J. Chem. Info. Comput. Sci. 2001,
41(1), 176-180. [PDF]
30. Rassokhin DN, Lobanov VS, Agrafiotis DK*. Nonlinear mapping of massive data
sets by fuzzy clustering and neural networks. J. Comput.
Chem. 2001, 22(4), 373-386. [PDF]
31. Agrafiotis DK*, Rassokhin DN, Lobanov VS. Multidimensional scaling and visualization of large
molecular similarity tables. J. Comput. Chem. 2001,
22(5), 488-500. [PDF]
32. Agrafiotis DK*, Rassokhin DN. Design and prioritization of plates for high-throughput screening. J.
Chem. Info. Comput. Sci. 2001, 41(3),
798-805. [PDF]
33. Agrafiotis DK*. Multiobjective optimization of
combinatorial libraries. IBM J. Res. Develop. 2001, 45(3/4),
545-566. [PDF]
34. Lobanov VS*, Agrafiotis
DK. Combinatorial networks. J. Mol. Graphics Modell.
2001, 19(6), 571-578. [PDF]
35. Agrafiotis DK, Lobanov VS*.
Multidimensional scaling of combinatorial libraries without explicit enumeration.
J. Comput. Chem. 2001, 22(14),
1712-1722. [PDF]
36. Izrailev S*, Agrafiotis DK.
Variable selection for QSAR by artificial ant colony systems. SAR and QSAR
in Environ. Res. 2002, 13, 417-423. [PDF]
37. Agrafiotis DK*, Rassokhin DN. A fractal approach for selecting an appropriate bin size for
cell-based diversity estimation. J. Chem. Info. Comput.
Sci. 2002, 42, 117-122. [PDF]
38. Lobanov VS*, Agrafiotis DK.
Scalable methods for the construction and analysis of virtual combinatorial
libraries. Combin. Chem. High-Throughput
Screen. 2002, 5, 167-178. [PDF]
39. Agrafiotis DK*, Cedeño W. Feature selection
for structure-activity correlation using binary particle swarms. J. Med.
Chem. 2002, 45, 1098-1107. [PDF]
40. Agrafiotis DK*, Lobanov VS, Salemme FR. Combinatorial informatics in the
post-genomics era. Nature Rev. Drug Discov. 2002,
1, 337-346. [PDF]
41. Agrafiotis DK*, Cedeño W, and Lobanov VS. On
the use of neural network ensembles in QSAR and QSPR. J. Chem. Info. Comput. Sci. 2002, 42, 903-911. [PDF]
42. Xu H*, and Agrafiotis DK. Retrospect and
prospect of virtual screening in drug lead discovery. Curr.
Topics Med. Chem. 2002, 2, 1305-1320. [PDF]
43. Agrafiotis DK*. Multiobjective optimization of
combinatorial libraries. J. Comput. Aid. Mol. Des. 2002, 16, 335-356.
[PDF]
44. Cedeño W, Agrafiotis DK. Combining particle
swarms and k-nearest neighbors for the development of quantitative
structure-activity relationships. Int. J. Comput.
Res. 2002, 11, 443-452. [PDF]
45. Cedeño W*, Agrafiotis DK. Application of niching particle swarms to QSAR and QSPR. Proceedings of
the 14-th European Symposium on QSAR, Bournemouth, UK, September 8-13, 2002.
[PDF]
46. Agrafiotis DK*,
Xu H. A self-organizing principle for learning nonlinear manifolds. Proc.
Natl. Acad. Sci. USA, 2002, 99, 15869-15872. [PDF]
47. Agrafiotis DK*. Stochastic proximity embedding. J. Comput. Chem. 2003, 24, 1215-1221. [PDF]
48. Agrafiotis DK*, Xu H. A geodesic framework for analyzing molecular
similarities. J. Chem. Info. Comput. Sci. 2003,
43, 475-484. [PDF]
49. Cedeño W*, Agrafiotis DK. Using particle
swarms for the development of QSAR models based on k-nearest neighbor and
kernel regression. J. Comput. Aid. Mol. Des. 2003,
17, 255-263. [PDF]
50. Rassokhin DN*, Agrafiotis DK. A modified update
rule for stochastic proximity embedding. J. Mol. Graphics Modell. 2003, 22, 133-140. [PDF]
51. M. Farnum, Xu H, Agrafiotis DK*. Exploring the nonlinear geometry of
sequence homology. Protein Sci. 2003, 12, 1604-1612. [PDF]
52. Xu H, Izrailev S, Agrafiotis DK*. Conformational sampling by
self-organization. J. Chem. Info. Comput. Sci. 2003,
43, 1186-1191. [PDF]
53. Xu H*, Agrafiotis DK. Nearest neighbor
search in general metric spaces using a tree data structure with a simple
heuristic. J. Chem. Info. Comput. Sci. 2003,
43, 1933-1941. [PDF]
54. Izrailev S*, Agrafiotis DK. A method for
quantifying and visualizing the diversity of QSAR models. J. Mol. Grphics Modell. 2004, 22,
275-284. [PDF]
55. Seierstad M*, Agrafiotis DK. A QSAR model of hERG binding using a large, diverse and internally
consistent training set. Chem. Biol. Drug. Des. 2006, 67(4),
284-296. [PDF]
56. Izrailev S, Zhu F, Agrafiotis DK*. A distance geometry heuristic for
expanding the range of geometries sampled during conformational search. J. Comput. Chem. 2006, 27(16), 1962-1969. [PDF]
57. Engels MFM*, Gibbs A,
Jaeger EP, Verbinnen D, Lobanov VS, Agrafiotis
DK. A clustering method for assessing the overlap between large
chemical libraries and its application to a recent acquisition. J. Chem.
Info. Model. 2006, 46, 2651-2660. [PDF]
58. Agrafiotis DK*, A. Gibbs, Zhu F, Izrailev S, Martin E. Conformational
boosting. Aust. J. Chem. 2006, 59, 874-878. [PDF]
59. Agrafiotis DK*, Bandyopadhyay D, Farnum M. Radial clustergrams:
visualizing the aggregate properties of hierarchical clusters. J. Chem.
Info. Model. 2007, 47, 69-75. [PDF]
60. Zhu F*, Agrafiotis DK. A self-organizing
superposition (SOS) algorithm for conformational sampling. J. Comput. Chem. 2007, 28, 1234-1239. [PDF]
61. Agrafiotis DK*, A. Gibbs, Zhu F, Izrailev S, and E. Martin.
Conformational sampling of bioactive molecules: a comparative study. J.
Chem. Info. Model. 2007, 47, 1067-1086. [PDF]
62. Agrafiotis DK*, Bandyopadhyay, Wegner JD, Van Vlijmen H. Recent advances
in chemoinformatics. J. Chem. Info. Model., 2007, 47,
1279-1293. [PDF]
63. Zhu F*, Agrafiotis DK. Recursive distance
partitioning algorithm for common pharmacophore identification. J. Chem.
Info. Model. 2007, 47, 1619-1625. [PDF]
64. Agrafiotis DK*, Bandyopadhyay, Carta DG, Knox
AJS, Lloyd DG. On the effects of permuted input on conformational sampling of druglike molecules: an evaluation of stochastic proximity
embedding (SPE). Chem. Biol. Drug Des. 2007, 70(2),
123-133. [PDF]
65. Agrafiotis DK*, Shemanarev M, Connolly PJ,
Farnum M, Lobanov VS. SAR maps: a new SAR visualization technique for medicinal
chemists. J. Med. Chem. 2007, 50(24), 5926-5937. [PDF]
66. Agrafiotis DK*, et al. Advanced Biological and Chemical Discovery (ABCD):
centralizing discovery knowledge in an inherently decentralized world. J.
Chem. Info. Model. 2007, 47, 1999-2014. [PDF]
67. Bandyopadhyay D, Agrafiotis DK*. A self-organizing algorithm for
molecular alignment and pharmacophore development. J. Comput.
Chem. 2008, 29, 965-982. [PDF]
68. Liu P*, Zhu F,
Rassokhin DN, Agrafiotis DK*. A self-organizing algorithm for modeling
protein loops. PLoS Comput. Biol.
2009, 5(8), e1000478. [PDF]
69. Kolpak J, Connolly
PJ, Lobanov VS, Agrafiotis DK*. Enhanced SAR maps: Expanding the data
rendering capabilities of a popular medicinal chemistry tool. J. Chem. Info. Model. 2009, 49, 2221-2230. [DOI]
70. Bonnet P, Agrafiotis
DK*, Zhu F, Martin EJ. Conformational analysis of macrocycles: finding what
common search methods miss. J. Chem.
Info. Model. 2009, 49, 2242-2259. [DOI]
71. G. Tresadern*, and Agrafiotis
DK. Conformational sampling with stochastic proximity embedding (SPE) and
self-organizing superimposition (SOS): Establishing reasonable parameters for
their practical use. J. Chem. Info. Model.
2009, 49, 27862800. [DOI]
72. Cepeda MS, Lobanov
VS, Farnum M, Weinstein R, Gates P, Agrafiotis DK, Stang P, Berlin JA.
Broadening access to electronic health care databases. Nat. Rev. Drug Discov. 2010, 9, 84. [DOI]
73. Liu P*, Agrafiotis
DK, Theobald DL. Fast determination of the optimal rotation matrix for
weighted superpositions. J. Comput. Chem. 2010, 31, 1561-1563. [DOI]
74. Agrafiotis DK*, Wiener JJM.
Scaffold Explorer: An interactive tool for organizing and mining SAR data
spanning multiple chemotypes. J. Med.
Chem. 2010, 53(13), 5002-5011. [DOI]
75. Agrafiotis DK*, Xu H, Zhu F,
Bandyopadhyay D, Liu P. Stochastic proximity embedding: methods and
applications. Mol. Inf. 2010, 29, 758-770. [DOI]
76. Liu P*, Agrafiotis
DK, Theobald DL. Rapid communication reply to
comment on: 'Fast determination of the optimal rotation matrix for
macromolecular superpositions. J. Comput. Chem. 2011, 32, 185-186. [DOI]
77. Tsantili-Kakoulidou A, Agrafiotis DK. Report on the 18-th
European symposium on quantitative structure-activity relationships. Expert Opin. Drug
Discovery. 2011, 6, 453-456. [DOI]
78. Agrafiotis DK*, Wiener JJM,
Skalkin A, Kolpak J. Single R-group polymorphisms (SRPs) and R-cliffs: An
intuitive framework for analyzing and visualizing activity cliffs in a single
analog series. J. Chem. Inf. Model.
In press. [DOI]
79. Tsantili-Kakoulidou A, Agrafiotis DK. 18th EuroQSAR: Perspectives on QSAR, molecular informatics and drug
design. Mol. Inf. 2011, 30, 8788. [DOI]
UNDER REVIEW
80. Liu P*, Agrafiotis
DK, Rassokhin DN. Power keys: a novel class of topological descriptors
based on exhaustive subgraph enumeration and their application in substructure
searching. Submitted.
81. Liu P*, Agrafiotis
DK, Rassokhin DN, Yang E. Accelerating chemical database searching through efficient
manipulation of lossless compressed fingerprints using graphics processing units
(GPUs). Submitted.
1. Agrafiotis DK, Bone R, Salemme FR, Soll R. System and
method for automatically generating chemical compounds with desired properties.
US Patent 5,463,564, October 31, 1995. [USPTO]
2. Agrafiotis DK, Bone R, Salemme FR, Soll R. System and
method for automatically generating chemical compounds with desired properties.
US Patent 5,574,656, November 12, 1996. [USPTO]
3. Agrafiotis DK, Bone R, Salemme FR, Soll R. System, method
and computer program for at least partially automatically generating chemical
compounds having desired properties. US Patent 5,684,711, November 4, 1997. [USPTO]
4. Agrafiotis DK, Bone R, Salemme FR Soll R. System, method
and computer program for at least partially automatically generating chemical
compounds with desired properties from a list of potential chemical compounds
to synthesize. US Patent 5,901,069, May 4, 1999. [USPTO]
5. Agrafiotis DK, Salemme FR. Method,
system, and computer program product for representing
similarity/dissimilarity between chemical compounds.
US Patent 6,295,514, September
25,2001. [USPTO]
6. Agrafiotis DK, Bone R, Salemme FR, Soll R. System, method
and computer program product
for identifying chemical compounds
with desired properties. US Patent 6,421,612, July
16,2002. [USPTO]
7. Agrafiotis DK, Bone R, Salemme FR, Soll R. Methodof generating chemical compounds having desired properties.
US Patent 6,434,490, August
13,2002. [USPTO]
8. Agrafiotis DK,
Lobanov VS, Salemme FR. System, method, and computer program product for
representing proximity data in a multidimensional space. US Patent 6,453,246,
September 17, 2002. [USPTO]
9. Dhanoa DS, Doller D, Meegalla S, Soll R, Agrafiotis
DK, Wisnewski N, Silver GM, Stinchcomb DT, Seward RL. Use of 1,3-substituted
pyrazol-5-yl sulfonates as pesticides". US
Patent 6,506,784, January 14, 2003. [USPTO]
10. Meegalla S, Agrafiotis DK, Dhanoa
D, Doller D, Soll R, Wisnewski N, Silver G, Stinchcomb
D, Seward RL, Sha D. 1-aryl-3-thioalkyl pyrazoles, and the synthesis thereof and use thereof as
insecticides. US Patent 6,518,266, February 11, 2003. [USPTO]
11. Agrafiotis DK,
Lobanov VS, Salemme FR. Method, system and computer program product for
nonlinear mapping of multidimensional data. US Patent 6,571,227, May 27, 2003. [USPTO]
12. Agrafiotis DK,
Lobanov VS, Salemme FR. Method and computer program product for designing
combinatorial arrays. US Patent 6,671,627, December 30, 2003. [USPTO]
13. Agrafiotis DK,
Lobanov VS, Salemme FR. Method, system, and computer program product for
encoding and building products of a virtual combinatorial library. US Patent
6,678,619, January 13, 2004. [USPTO]
14. Lobanov VS, Agrafiotis DK, Salemme FR. Method,
system, and computer program product for determining properties of
combinatorial library products from features of library building blocks. US
Patent 6,834,239, December 21, 2004. [USPTO]
15. Agrafiotis DK,
Rassokhin DN, Lobanov VS, Salemme FR. System, method, and computer program
product for representing object relationships in a multidimensional space. US
Patent 7,039,621, May 2, 2006. [USPTO]
16. Agrafiotis DK,
Lobanov VS, Salemme FR. Method, system, and computer program product for
analyzing combinatorial libraries. US Patent 7,054,757, June 13, 2006. [USPTO]
17. Agrafiotis DK,
Lobanov VS, Salemme FR. Method, system and computer program product for
non-linear mapping of multi-dimensional data. US Patent 7,117,187, October 3, 2006. [USPTO]
18. Agrafiotis DK,
Rassokhin DN, Lobanov VS, Salemme FR. System, method, and computer program
product for representing object relationships in a multidimensional space. US
Patent 7,139,739, November 21, 2006. [USPTO]
UNDER REVIEW
Several
patent applications are currently under review.
SELECTED
1. Agrafiotis DK, Jaeger EP. DirectedDiversity: an operating
system for combinatorial chemistry. 212-th
ACS National Meeting, March 24-28, 1996, New Orleans, LA.
2. Agrafiotis DK. Stochastic algorithms for assessing molecular diversity. 213-th ACS National Meeting,
April 13-17, 1997, San Francisco, CA.
3. Agrafiotis DK. Computer-aided combinatorial drug design. 9-th International
Congress of Quantum Chemistry, June 3-7, 1997, Savannah, GA.
4. Agrafiotis DK. Systems and methods for designing combinatorial chemistry experiments.
Gordon Conference on QSAR, August 3-8, 1997, Tilton, NH.
5. Agrafiotis DK. Thinking machines in drug design: the challenge of combinatorial
chemistry. DuPont Central Research & Development, Wilmington, DE, December 17, 1997.
6. Agrafiotis DK, Lobanov VS. Bridging the gap between diversity and QSAR. 215-th ACS
National Meeting, March 29 - April 2, 1998, Dallas, TX.
7. Agrafiotis DK, Lobanov VS. A rational approach for combinatorial drug design. Computational
Approaches to the Design and Analysis of Combinatorial Libraries, MGMS/CSA
Meeting, April 14-16, 1998, Sheffield, England.
8. Agrafiotis DK. Lobanov VS. Meta-QSAR. 217-th ACS National Meeting, March
21-25, 1999, Anaheim, CA.
9. Agrafiotis DK. PacifiChem 2000, Symposium on Mathematical
Aspects of Drug Design, Honolulu, Hawaii,
December 14-18, 2000.
10. Agrafiotis DK. Multidimensional scaling of massive data sets. DIMACS Series on
Computational Molecular Biology, Rutgers University, June 21-22, 2001.
11. Agrafiotis DK.
Stochastic proximity embedding. 2002 Gordon Conference on Computational
Chemistry, June 30-July 5, 2002, Colby-Sawyer College, NH.
12. Agrafiotis DK.
Molecular informatics in the new millennium. Princeton University,
February 21, 2003, Princeton, NJ.
13. Agrafiotis DK, Xu
H. A self-organizing algorithm for extracting the
intrinsic dimensionality of large high-dimensional data. 225-th ACS National Meeting, March
23-27, 2003, New
Orleans, LA.
14. Agrafiotis DK.
New algorithms for the analysis of large data sets and their application in
molecular design. Cornell University, April 25, 2003, Ithaca, NY.
15. Agrafiotis DK.
A self-organizing alternative to distance geometry. Accelrys
World, March 8-10, 2004, San Diego, CA.
16. Agrafiotis DK.
Molecular informatics for the new drug discovery enterprise. Chemistry &
Biology: Partners in Decoding the Genome, NIH, March 15-16, 2004, Bethesda, MD.
17. Agrafiotis DK.
Molecular informatics for the new drug discovery enterprise. Indiana
University, March 24, 2004, Bloomington, IN.
18. Agrafiotis DK. Visualizing structure-activity relationships in ABCD. 230-th ACS National Meeting, August
28-September 1, 2005, Washngton, DC.
19. Agrafiotis DK. Computational tools for the design and analysis of massive
combinatorial libraries. Gordon Conference on Combinatorial and High Throughput
Materials Development, August 14-19, 2005, Oxford,
UK.
20. Agrafiotis DK.
Design and analysis of large chemical libraries for lead discovery &
optimization. EMBL/EBI Conference on Therapeutic Applications of
Computational Biology, September 4-6, 2005, Hinxton,
UK.
21. Agrafiotis DK.
New algorithms for the analysis of large data sets and their application in
molecular design. University of Toronto, September 22, 2005, Toronto,
Canada.
22. Agrafiotis DK.
A new clustering algorithm for general metric spaces. 1-st German Conference
on Chemoinformatics, November 13-15, 2005, Goslar, Germany.
23. Agrafiotis DK.
Modeling complexity: from stochastic proximity embedding to ABCD. University
of Erlangen, November 16, 2005, Erlangen, Germany.
24. Agrafiotis DK.
A self-organizing principle for modeling proximity data. Pacifichem
2005, December 15-20, 2005, Honolulu, HI.
25. Agrafiotis DK.
ABCD: centralizing .data in an inherently decentralized world. Plenary Talk,
Smart Lab 2007, February 27-28, 2007, London, UK.
26. Agrafiotis DK.
Plenary Talk, Discovery Knowledge & Informatics, April 24-25,
2007, Amsterdam, The Netherlands.
27. Agrafiotis DK.
Gibbs A, Zhu F, Martin E. Advances in conformational sampling. 233-rd ACS
National Meeting, March 25-29, 2007, Chicago, IL.
28. Agrafiotis DK.
New algorithms for mining large data sets. MBI Chemogenomics Workshop,
Mathematical Biosciences Institute, Ohio State University, May 8-9, 2007,
Columbus, OH.
29. Agrafiotis DK.
Plenary Talk, SIAM Conference on Mathematics for Industry: Challenges
& Frontiers, October 9-11, 2007, Philadelphia, PA.
30. Agrafiotis DK. Towards a unifying platform for discovery,
translational and clinical informatics. Plenary Talk, 2009
Life Science Technology Symposium, September 30, 2009, Princeton, NJ.
31. Agrafiotis DK. Discovery informatics on an industrial scale The
past, present and future of ABCD. Keynote Talk, Annual Biocomputing Day, University of New
Mexico, March 27, 2009.
32. Agrafiotis DK. Discovery informatics on an industrial scale The
past, present and future of ABCD. Merck
& Co., April 23, 2009.
33. Agrafiotis DK. Discovery informatics on an industrial scale The
past, present and future of ABCD. Novartis,
May 26, 2009, Boston, MA.
34. Agrafiotis DK. Discovery informatics on an industrial scale The
past, present and future of ABCD. Sanofi-Aventis,
December 7, 2009, Bridgewater, NJ.
35. Agrafiotis DK. SPE and SOS: Two robust and universally applicable
conformational search algorithms. 239-th
ACS National Meeting, March 21-25, 2010, San Francisco, CA.
36. Agrafiotis DK. A unifying framework for integrative informatics. IEEE Conference in Bioinformatics &
Bioengineering, June 1-2, 2010, Philadelphia, PA.
37. Agrafiotis DK. 15 years in chemical
informatics: lessons from the past, ideas for the future. Invited Lecture, JCIM 50-th
Anniversary Symposium, 240-th ACS National Meeting, August
22-26, 2010, Boston, MA.
38. Agrafiotis DK. R-Cliffs: Activity
cliffs within a single analog series. 240-th ACS National Meeting, August
22-26, 2010, Boston, MA.
39. Agrafiotis DK. Visual (Q)SAR: SAR maps,
scaffold trees, and R-cliffs. EuroQSAR 2010,
September 19-24, Rhodos, Greece.
40. Agrafiotis DK. UCLA,
Institute for Pure and Applied Mathematics, April 4-8, 2011.