2004
Ross
A. Overbeek
Fellowship for Interpretation
of Genomes
Burr Ridge, IL 60527
Phone: 630-325-4178,
Education
1971 - Ph.D. The Pennsylvania State University
1970 - M.S. The Pennsylvania State
University
1970 - B.Ph. Grand Valley State College
Experience
2003 - Founding
Member, Bioinformatics
Fellowship
for Interpretation of Genomes
1999 - 2003 Vice President
Bioinformatics
Integrated
Genomics, Inc.
1988 - 1999 Senior Computer
Scientist
Mathematics
and Computer Science Division
Argonne
National Laboratory
1983 - 1988 Computer Scientist
Mathematics
and Computer Science Division
Argonne
National Laboratory
1980 - 1983 Professor
Northern
Illinois University
1974 - 1980 Associate Professor
Northern
Illinois University
1971 - 1974 Assistant Professor
Northern
Illinois University
Books
1. Singletary,
W. E. and R. Overbeek, ANS COBOL: A Pragmatic Approach, McGraw-Hill Company , New York , 1975.
2. Overbeek,
R. and W. E. Singletary, An Introduction to IBM 360/370 Assembler Language
Using ASSIST, SRA, 1976.
3. Wos,
Larry, Ross Overbeek, Ewing Lusk, and Jim Boyle, Automated Reasoning:
Introduction and Applications, Prentice‑Hall,
Englewood Cliffs, New Jersey, 1984.
4. Boyle,
Jim, Ralph Butler, Terry Disz, B. Glickfeld, E. L. Lusk, R. A. Overbeek, J.
Patterson, and R. Stevens, Portable Programs for Parallel Processors, Holt, Rinehart, and Winston, New York, New York, 1987.
Journal Articles and Book Chapters
1. Hughes,
C. B., R. Overbeek, and W. E. Singletary, The many‑one equivalence of
some general combinatorial decision problems, Bull. Amer. Math. Soc., 77, pp. 467‑472,
1971.
2. Overbeek,
R., The representation of many‑one degrees by decision problems of Turing
Machines, Proceedings of the London Mathematical Society, 26, pp. 162‑183,
1973.
3. Overbeek,
R., The representation of many‑one degrees by the word problem for Thue
Systems, Proceedings of the London Mathematical Society, 26, pp. 184‑192,
1973.
4. Overbeek,
R., A new class of automated theorem‑proving algorithms, Journal of
the ACM, 21, pp. 191‑200, 1974.
5. Henschen,
L., L. Wos, and R. Overbeek, A theorem proving language for experimentation, Communications
of the ACM, 17, no. 6, pp. 308‑314, June 1974.
6. Overbeek,
R., An implementation of hyper‑resolution, Computers and Mathematics
with Applications, 1, pp. 201‑214,
1975.
7. McCharen,
J., R. Overbeek, and L. Wos, Complexity and related enhancements for automated
theorem‑proving programs, Computers and Mathematics with Applications,
2, pp. 1-16, 1976.
8. McCharen,
J., R. Overbeek, and L. Wos, Problems and experiments for and with automated
theorem‑proving programs, IEEE Transactions on Computers, C‑25,
no. 8, pp. 773‑782, 1976.
9. Lusk,
E. and R. Overbeek, A DML for entity relationship models, Entity-Relationship
Approach to Systems Analysis and Design,
ed. P. P. Chen, North-Holland, Amsterdam, 1980.
10. Lusk,
E. and R. Overbeek, Experiments with resolution-based theorem-proving
algorithms, Computers and Mathematics with Applications, 8, no. 3, pp. 141-152, 1982.
11. Lusk,
E., R. Overbeek, and G. Petrie, Item tracking entity- relationship models, Entity-Relationship
Approach to Information Modeling and Analysis, ed. Peter P. Chen, pp. 215-236, North-Holland, Amsterdam, 1983.
12. Margrave,
G., E. Lusk, and R. Overbeek, Tools for the creation of IMS database designs
from entity- relationship diagrams, Entity-Relationship Approach to Software
Engineering, ed. Carl G. Davis,
Sushil Jajodia, Peter A. Ng, and Raymond T. Yeh, pp. 501-515, North-Holland,
New York, 1983.
13. Lusk,
E. L. and Ross A. Overbeek, Comment atteindre le milliard d'inferences par
seconde, Intelligence Artificielle et Productique, pp. 5-7, Novembre 1984.
14. Gabriel,
J., T. Lindholm, E. L. Lusk, and R. A. Overbeek, Logic programming on the HEP,
Parallel MIMD Computation: The HEP Supercomputer and its Applications, ed. J. S. Kowalik, The MIT Press, 1985.
15. Lusk,
E. L. and R. A. Overbeek, Use of monitors in FORTRAN: A tutorial on the
barrier, self-scheduling DO-loop, and askfor monitors, Parallel MIMD
Computation: The HEP Supercomputer and its Applications, ed. J. S. Kowalik, The MIT Press, 1985.
16. Lusk,
E. L. and R. A. Overbeek, Non-horn problems, Journal of Automated Reasoning,
1, no. 1, pp. 103-114, 1985.
17. Lusk,
E. L. and R. A. Overbeek, Reasoning about equality, Journal of Automated
Reasoning, 1, no. 2, pp. 209-227,
1985.
18. Lusk,
E. L., R. A. Overbeek, and B. Parrello, General ledger systems and the design
of entity-relationship models, Journal of Data and Knowledge Engineering, 1, pp. 155-180, North-Holland, 1985.
19. Clausing,
J., R. Hagstrom, E. Lusk, and R. A. Overbeek, A technique for achieving
portability among multiprocessors: Implementation on the Lemur, Parallel
Computing, 2, no. 2, pp. 137-162,
June 1985.
20. Boyer,
R., E. Lusk, W. McCune, R. Overbeek, M. Stickel, and L. Wos, Set theory in
first-order logic: clauses for Godel's axioms, Journal of Automated
Reasoning, 2, no. 3, pp. 277-327,
1986.
21. Gfickfeld,
B. and R. Overbeek, A foray into combinatory logic, Journal of Automated
Reasoning, 2, no. 4, pp. 419-431,
December 1986.
22. Lusk,
E. L. and R. A. Overbeek, A minimalist approach to portable, parallel
programming, The Characteristics of Parallel Algorithms, ed. Leah H. Jamieson, Dennis B. Gannon, and Robert
J. Douglass, pp. 351-362, The MIT Press, Cambridge, Massachusetts, 1987.
23. Lucier,
B. J. and R. Overbeek, Parallel adaptive numerical schemes for hyperbolic
systems of conservation laws, SIAM J. Sci. Stat. Comput., 8, no. 2, pp s203-s219, March 1987.
24. Glickfeld,
B. and R. Overbeek, Geometric representation of scheduling constraints: a
simplied approach to multiprocessing, Parallel Computing, 6, pp. 325-337, 1988.
25. Butler,
R., T. Butler, I. Foster, N. Karonis, R. Olson, R. Overbeek, N. Pfluger, M.
Price, and S. Tuecke, Aligning genetic sequences, Strand: New Concepts in
Parallel Programming, Prentice-Hall,
Englewood Cliffs, New Jersey, 1989.
26. Kazic,
T., E. Lusk, R. Olson, R. Overbeek and S. Tuecke, Prototyping Databases in
Prolog, The Practice of Prolog,
MIT Press, Cambridge, Massachusetts, 1990.
27. Singh,
A. K. and R. Overbeek, Derivation of Efficient Parallel Programs: an Example
from Genetic Sequence Analysis, International Journal of Parallel
Programming, 18, no. 6, pp. 447-484,
1989.
28. Lusk,
E., R. Butler, T. Disz, G. Olson, R. Overbeek, Stevens, Warren, Calderwood, P.
Szeredi, S. Hiridi, P. Brand, M. Carlsson, Ciepielewski, and Hausman, The
Aurora Or-Parallel Prolog System, New Generation Computing, 7, pp. 243-271, 1990
29. Jindal,
A., R. Overbeek, and W. Kabat Exploitation of Parallel Processing for
Implementing High-Performance Deduction Systems, Journal of Automated Reasoning
(to appear)
30. Winker,
S., R. Overbeek, C. R. Woese, G. J. Olsen, and N. Pfluger, Structure Detection
through Automated Covariance Search, CABIOS 4, no. 6 (1990) 365-371 (also MCS-P168-0890)
31. Olsen,
G. J., R. Overbeek, N. Larsen, and C.R. Woese, The Ribosomal Database Project:
Updated Description Nucleic Acids Res. 19, (1991) 4817
32. Overbeek,
R. and I. Foster, Aligning Multiple RNA Sequences Automated Reasoning:
Essays in Honor of Woody Bledsoe, pp.
231‑248, ed. Robert S. Boyer, Kluwer Academic Pub., 1991
33. Michaels,
G. S., R. Taylor, P. Munson, R. Hagstrom, M. Price, and R. Overbeek, Searching
for Genomic Organizational Motifs: Explorations of the Escherichia coli Chromosome, Computers in Chemistry (in press, 1992)
34. Olsen,
G. J., H. Matsuda, R. Hagstrom, and R. Overbeek fastDNAml: a tool for
construction of phylogenetic trees of DNA sequences using maximum likelihood, CABIOS, 1993
35. Larsen,
N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L.
Marsh, and C. R. Woese, The Ribosomal Database Project Nucleic Acids Res. 21, (1993) 3021‑3023
36. Olsen, G. J., C. R. Woese, and R. Overbeek, The Winds
of (Evolutionary) Change: Breathing New Life into Microbiology, Journal of
Bacteriology, Jan 1994, pp.1‑6
37. Hagstrom, J. N., R. Hagstrom, R. Overbeek, Morgan
Price, and Linus Schrage, Maximum Likelihood Genetic Sequence Reconstruction
from Oligo Networks, Volume 24, pp.
297‑302, August 1994.
38. Smith, S. W., R. Overbeek, C. R. Woese, W. Gilbert,
and P.M. Gillevet, The Genetic Data ERnvironment, an Expandable GUI for
Multiple Sequence Analysis, CABIOS, 10,
671‑675, 1994
39. Kagawa, H. K., J. Osipiuk, N. Maltsev, R. Overbeek,
E. QuaiteRandall, A. Joachimiak,
and J. D. Trent, The 60 kDa Heat Shock Proteins in the Hyperthermophilic
Archaeon Sulfolobus shibatae, Journal of Molecular Biology, 253, 712‑725, 1995
40. Selkov, E., S. Basmanova, I. Goryanin, Y. Gretchkin,
T. Gaasterland, N. MaJtsev, V. Nenashev, R. Overbeek, E. Panyushkina, L.
Pronevitch, E. Selkov Jr., and 1. Yunus, The Metabolic Pathway Collection from
EMP: the Enzymes and Metabolic Pathways Database, Journal of Nucleic Acids
Research, Vol. 24, 1, 26‑28,
January, 1996
41. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M.
J. McCaughey, and C. R. Woese, The Ribosomal Database Project (RDP), Journal
of Nucleic Acids Research, Vol. 24,
1, 82‑85, January, 1996
42. Bult,
C. J., et al., Complete genome sequence of the methanogenic archeon Methanococcus
jannaschii. Science 273: 1058‑1073,
1996
43. Selkov,
E., M. Galimova, I. Goryanin, Y. Gretchkin, N. Ivanova, Y. Komarov, N. Maltsev,
N. Mikhailova, V. Nenashev, R. Overbeek, E. Panyushkina, L. Pronevitch, and E.
Selkov Jr., The Metabolic Pathway Collection: an Update, Journal of Nucleic
Acids Research, Vol. 25, 1, 39‑42, January, 1997
44. Maidak,
B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese,
The RDP(Ribosomal Database Project), Journal of Nucleic Acids Research, Vol.
25, 1, 109‑110, January, 1997
45. Overbeek,
R., N. Larsen, W. Smith, N. Maltsev, and E. Selkov, Representation of function:
the next step, Published on‑line: 31 January 1997; Gene 191(l): GC1‑9
46. Selkov, E., N. Maltsev, G. Olsen, R. Overbeek, C.
Woese, and W. B. Whitman,. A Reconstruction of the Metabolism of Methanococcus
jannaschii from Sequence Data. GENE‑COMBIS
197, no. 1‑2,1997, GC10‑25
47. Selkov, E, N. Maltsev,
G. J. Olsen, R. Overbeek, and W. B. Whitman, A reconstruction of the
metabolism of Methanococcus jannaschii from sequence data, Gene 197, pp GC11-G26, 1997
48. Dsouza, M., N. Larsen,
and R. Overbeek, Searching for patterns in genomic data, Trends Genet. 13, pages 497-498, 1997
49. Deckert, G., P. V.
Warren, T. Gaasterland, W. G. Young, A. L. Lenox, D. E. Graham, R. Overbeek, M.
A. Snead, M. Keller, M. Aujay, R. Huber, R. A. Feldman, J. M. Short, G. J.
Olsen, and R. V. Swanson, The complete genome of the hyperthermophilic
bacterium Aquifex aeolicus, Nature 392, pages 353-358, 1998
50.
Maidak,
B. L., J. R. Cole, C. T. Parker Jr, G. M. Garrity, N. Larsen, B. Li, T. G.
Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt,
J. M. Tiedje, and C. R. Woese, A new version of the RDP (Ribosomal Database
Project), Nucleic Acids Res. Jan 1;27(1), pages 171-173., 1999
51.
Overbeek,
R., M. Fonstein, M. D'Souza, G. D. Pusch, and N. Maltsev, Use of contiguity on
the chromosome to predict functional coupling. In Silico Biol. 1998;1(2):93-108.
52.
Overbeek,
R., M. Fonstein, M. D'Souza, G. D. Pusch, and N. Maltsev, The use of gene
clusters to infer functional coupling, Proc Natl Acad Sci USA 96 (6),pages 2896-2901, 1999
53.
Kyrpides,
N., R. Overbeek, and C. Ouzounis, Universal protein families and the functional
content of the last universal common ancestor, Mol Evol. 1999 Oct;49(4):413-23
54.
Overbeek,
R., N. Larsen, G. D. Pusch, M. D'Souza, E. Selkov, N. Kyrpides, M. Fonstein, N.
Maltsev, and E. Selkov, WIT: integrated system for high-throughput genome
sequence analysis and metabolic reconstruction, Nucleic Acids Res. 2000 Jan
1;28(1):123-5
55.
Selkov,
E., R. Overbeek, Y. Kogan, L. Chu, V. Vonstein, D. Holmes, S. Silver, R.
Haselkorn, and M. Fonstein, Functional analysis of gapped microbial genomes:
Amino acid metabolism of Thiobacillus ferrooxidans, Proc Natl Acad Sci
USA. 2000 Mar 28;97(7):3509-3514.
56.
Graham,
D. E., R. Overbeek, G. J. Olsen, and C. R. Woese, An archaeal genomic
signature, Proc Natl Acad Sci USA. 2000 Mar 28;97(7):3304-3308.
57.
Overbeek,
R., Genomics: what is realistically achievable? Genome Biol. 2000;1(2):COMMENT 2002.
58.
Kyrpides,
N. C., C. A. Ouzounis, I. Iliopoulos, V. Vonstein, and R. Overbeek, Analysis of
the Thermotoga maritima genome combining a variety of sequence similarity and
genome context tools. Nucleic Acids Res. 2000 Nov 15;28(22):4573-6.
59.
Daugherty,
M., V. Vonstein, R. Overbeek, and A. Osterman, Archaeal shikimate kinase, a new
member of the GHMP-kinase family. J Bacteriol. 2001 Jan;183(1):292-300.
60.
Graham,
D. E., N. Kyrpides, I. J. Anderson, R. Overbeek, and W. B. Whitman, Genome of Methanocaldococcus
(Methanococcus) jannaschii. Methods Enzymol. 2001;330:40-123.
61.
DelVecchio,
V. G., V. Kapatral, R. J. Redkar, G. Patra, C. Mujer, T. Los, N. Ivanova, I.
Anderson, A. Bhattacharyya, A. Lykidis, G. Reznik, L. Jablonski, N. Larsen, M.
D'Souza, A. Bernal, M. Mazur, E. Goltsman, E. Selkov, P. H. Elzer, S. Hagius,
D. O'Callaghan, J. J. Letesson, R. Haselkorn, N. Kyrpides, and R. Overbeek, The
genome sequence of the facultative intracellular pathogen Brucella
melitensis.
Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):443-8.
62.
Kapatral,
V., I. Anderson, N. Ivanova, G. Reznik, T. Los, A. Lykidis. A. Bhattacharyya,
A. Bartman, W. Gardner, G. Grechkin, L. Zhu, O. Vasieva, L. Chu, Y. Kogan, O.
Chaga, E. Goltsman, A. Bernal, N. Larsen, M. D'Souza, T. Walunas, G. Pusch, R.
Haselkorn, M. Fonstein, N. Kyrpides and R. Overbeek, Genome sequence and
analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J
Bacteriol. 2002 Apr;184(7):2005-18.
63.
Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA,
Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard
T, Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R,
Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G.
The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and
archaea. J Mol Microbiol
Biotechnol. 2002 Jul;4(4):453-61.
64.
Bhattacharyya A, Stilwagen S, Ivanova N, D'Souza M, Bernal A,
Lykidis A, Kapatral V, Anderson I, Larsen N, Los T, Reznik G, Selkov E Jr,
Walunas TL, Feil H, Feil WS, Purcell A, Lassez JL, Hawkins TL, Haselkorn R,
Overbeek R, Predki PF, Kyrpides NC. Whole-genome comparative analysis of three phytopathogenic Xylella
fastidiosa strains. Proc Natl Acad Sci U S A. 2002 Sep
17;99(19):12403-8. Epub 2002 Aug 30.
65.
Bhattacharyya A, Stilwagen S, Reznik G, Feil H, Feil WS, Anderson
I, Bernal A, D'Souza M, Ivanova N, Kapatral V, Larsen N, Los T, Lykidis A,
Selkov E Jr, Walunas TL, Purcell A, Edwards RA, Hawkins T, Haselkorn R,
Overbeek R, Kyrpides NC, Predki PF. Draft sequencing and comparative genomics of Xylella
fastidiosa strains reveal novel biological
insights. Genome Res. 2002
Oct;12(10):1556-63.
66. Klaenhammer
T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou
S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols
P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L,
Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D,
Sorokin A, Steele J, O'Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R. Discovering
lactic acid bacteria by genomics. Antonie
Van Leeuwenhoek. 2002 Aug;82(1-4):29-58.
Review.
67.
Jenkins
C, Samudrala R, Anderson I, Hedlund BP, Petroni G, Michailova N, Pinel N,
Overbeek R, Rosati G, Staley JT. Genes for the cytoskeletal protein tubulin in the bacterial
genus Prosthecobacter. Proc Natl Acad Sci U S A. 2002 Dec
24;99(26):17049-54. Epub 2002 Dec 16.
68. Overbeek R, Larsen N,
Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D,
Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova
N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. The ERGO
genome analysis and discovery system.
Nucleic Acids Res. 2003 Jan 1;31(1):164-71.
69. Osterman A,
Overbeek R. Missing genes
in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol. 2003 Apr;7(2):238-51. Review.
70. Ivanova N,
Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A,
Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N,
D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD,
Overbeek R, Kyrpides N. Genome
sequence of Bacillus cereus and comparative
analysis with Bacillus anthracis. Nature. 2003 May 1;423(6935):87-91.
71. Kazakov AE,
Vassieva O, Gelfand MS, Osterman A, Overbeek R.
Bioinformatics classification and functional
analysis of PhoH homologs. In
Silico Biol. 2003;3(1-2):3-15. Epub 2002
Dec 30.
72.
Kapatral V, Ivanova N, Anderson I, Reznik G, Bhattacharyya A,
Gardner WL, Mikhailova N, Lapidus A, Larsen N, D'Souza M, Walunas T, Haselkorn
R, Overbeek R, Kyrpides N. Genome
analysis of F. nucleatum sub spp vincentii and its comparison
with the genome of F. nucleatum ATCC 25586. Genome Res. 2003
Jun;13(6A):1180-9.
73.
Overbeek,
R., Devine, D., and Vonstein, V. Curation Is Forever: Comparative Genomics
Approaches to Functional Annotation. TARGETS 2003 2:138-146
74.
Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty
MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V,
D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL,
Oltvai ZN, Osterman AL.
Experimental determination and system level analysis
of essential genes in Escherichia coli MG1655. J Bacteriol. 2003 Oct;185(19):5673-84.
75.
Farahi K, Pusch GD, Overbeek R, Whitman WB.
Detection of lateral gene transfer
events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances
method. J Mol Evol. 2004
May;58(5):615-31.
Articles in
Published Proceedings
1. Lusk,
E. and R. Overbeek, Data structures and control architecture for the
implementation of theorem‑proving programs, Proceedings of the Fifth
Conference on Autornated Deduction, Springer‑Verlag Lecture Notes in
Computer Science, Vol. 87, ed. Robert
Kowalski and Wolfgang Bibel, pp. 232‑249, Springer‑Verlag, New
York, 1980.
2. Henschen,
L., R. Overbeek, and L. Wos, Hyperparamodulation: A refinement of
paramodulation, Proceedings of the Fifth Conference on Automated Deduction,
Springer‑Verlag Lecture Notes in Computer Science, Vol. 87, ed. Robert Kowalski and Wolfgang Bibel, pp. 208‑219,
Springer‑Verlag, New York, July 1980.
3. Lusk,
E., W. McCune, and R. Overbeek, Logic machine architecture: inference
mechanisms, Proceedings of the Sixth Conference on Automated Deduction,
Springer Verlag Lecture Notes in Computer Science, Vol. 138, ed. D. W. Loveland, pp. 85‑108, Springer‑Verlag,
New York, 1982.
4. Lusk,
E., W. McCune, and R. Overbeek, Logic machine architecture: kernel functions, Proceedings
of the Sixth Conference on Automated Deduction, Springer Verlag Lecture Notes
in Computer Science, Vol. 138, ed. D.
W. Loveland, pp. 70‑84, Springer‑Verlag, New York, 1982.
5. Lusk,
E. L. and R. A. Overbeek, A portable environment for research in automated
reasoning, Proceedings of the 7th International Conference on Automated
Deduction, Springer‑Verlag Lecture Notes in Computer Science, Vol. 170, ed. R. E. Shostak, pp. 43‑52, Springer‑Verlag,
New York, 1984.
6. Lusk,
E. L. and R. A. Overbeek, Multiprocessing using macro packages that implement
monitors, Proceedings for the Argonne Workshop on Programming the Next
Generation of Supercomputers, pp. 91‑108,
Mathematics and Computer Science Division, Argonne National Laboratory, October
1984.
7. Colley,
R., S. Seeman, D. Smith, J. Gabriel, E. L. Lusk, and R. A. Overbeek, An entity‑relationship
model for nuclear power plants, Proceedings of the 1985 International
Topical Meeting on Computer Applications for Nuclear Power Plant Operation and
Control, pp. 765‑770, Tri‑Cities,
Washington, 1985.
8. Lusk,
E. L. and R. A. Overbeek, The role of multiprocessors in the nuclear power
industry: Comments on Determining Factors, Proceedings of the 1985
International Topical Meeting on Computer Applications for Nuclear Power Plant
Operation and Control, pp. 771‑775,
Tri‑Cities, Washington, 1985.
9. Lusk,
E. L. and R. A. Overbeek, Databases and automated reasoning, Proceedings of
the 1985 International Topical Meeting
on Computer Applications for Nuclear Power Plant Operation and Control, pp. 604,610, Tri‑Cities, Washington, 1985.
10. Lusk,
E. L. and R. A. Overbeek, The tradeoffs among portability, complexity, and
efficiency in multiprocessing environments, Proceedings of the Workshop on
Parallel Processing Using the Heterogeneous Element Processor, pp. 245‑260, Norman, Oklahoma, March 1985.
11. Butler,
R., E. Lusk, W. McCune, and R. Overbeek, Parallel logic programming for numeric
applications, Proceedings of the Third Conference on Logic Programming,
Springer‑ Veriag Lecture Notes in Computer Science, Vol. 225, ed. Ehud Shapiro, pp. 375‑388, Springer‑Verlag,
New York, 1986.
12. Lusk,
E., W. McCune, R. Overbeek, and R. Butler, Paths to high‑performance
automated theorem proving, Proceedings of the 8th International Conference
on Automated Deduction, Springer‑Verlag Lecture Notes in Computer
Science, Vol. 230, ed. J. H.
Sickmann, pp. 588‑597, Springer‑Verlag, New York, 1986.
13. Disz,
T., E. Lusk, and R. Overbeek, Experiments with OR‑parallel logic
programs, Proceedings of the 4th International
Conference on Logic Programming, pp.
576‑600, Melbourne, 1987.
14. Lusk,
E. L. and R. A. Overbeek, Automated reasoning and knowledge base design in the
scientific programming environment, Problem Solving Environments for
Scientific Computing, ed. B. Ford and
F. Chatelin, pp. 83‑96, New York, 1987.
15. Carlsson,
M., K. Danhof and R. Overbeek A Simplified approach to the implementation of
AND‑parallelism in an OR‑parallel environment, Logic Programming:
Proceedings of the Fifth International Conference and Symposium, ed. Robert A. Kowalski and Kenneth A. Bowen pp. 1565‑1577,
The MIT Press, Cambridge, Massachusetts, 1988.
16. Butler,
R., T. Disz, E. L. Lusk, R. Olson, R. Overbeek and R. Stevens, Sceduling OR‑parallelism:
an Argonne Perspective Logic Programming: Proceedings of the Fifth
International Conference and Symposium, ed.
Robert A. Kowalski and Kenneth A. Bowen pp. 1590‑1608, The MIT Press,
Cambridge, Massachusetts, 1988.
17. Lusk
E. L., R. Butler, T. Disz, R. Overbeek, R. Stevens, D. H. D. Warren, A.
Calderwood, P. Szeredi, S. Haridi, P. Brand and M. Carlsson, The Aurora OR‑Parallel
Prolog System Proceedings of the International Conference on Fifth Generation
Computer Systems, pp. 819‑830,
Institute for New Generation Computer Technology, Tokyo,1988
18. Wos,
L., S. Winker, W. McCune, R. Overbeek, E. Lusk, R. Stevens, and R. Butler,
Automated Reasoning Contributes to Mathematics and Logic Proceedings of the
10th International Conference on
Automated Deduction, Springer‑ Verlag Lecture Notes in Computer Science,
Vol. 449, ed. Mark Stickel, pp. 485‑499,
Springer‑Verlag, New York, 1990.
19. Foster
and R. Overbeek, Experiences with bilingual parallel programming Proc. 5th
Distributed Memory Computer Conference, IEEE
Press, pp. 1137‑1146, 1990.
20. Foster
and R. Overbeek, Bilingual parallel programming, Proceedings of the 3rd
Workshop on Parallel Languages and Compilers, MIT Press, 1990.
21. R.
Butler, Foster, A. Jindal, and R. Overbeek, A high‑ performance parallel
theorem prover Proceedings of the 10th International Conference on Automated
Deduction, Springer‑Verlag, New
York, 1990.
22. Michaels,
G. S., R. Taylor, R. Hagstrom, M. Price, and R. Overbeek, Comparative Analysis
of Genomic Data: a global look at structural and regulatory features Proceedings
of the Second International Conference of Bioinformnaties and Complex Genome
Analysis, ed. Hua A. Lim, World
Scientific Publishing Co., River Edge, NJ, 1992 (in press)
23. Kaoru,
Y., C. Smith, T. Kazic, G. Michaels, R. Taylor, D. Zawada, R. Hagstrom, and
Ross Overbeek, Towards a Human Genome Encyclopedia Proceedings of the
International Conference on Fifth Generation Computer Systems 1992, pages 307‑320, Tokyo, Japan, June 1‑5,
1992
24. Gaasterland,
Terry and Ross Overbeek, Genetic Sequence Analysis: the Grand Challenge Proceedings
of the Third International Conference on Practical Applications of Prolog, pages 245‑258, Paris, France, April, 1995
25. Bult
CJ; White 0; Olsen GJ; Zhou L; Fleischmann RD; Sutton GG; Blake JA; FitzGerald
LM; Clayton RA; Gocayne JD; Kerlavage AR; Dougherty BA; Tomb JF; Adams MD;
Reich CI; Overbeek R; Kirkness EF; Weinstock KG; Merrick JM; Glodek A; Scott
JL; Geoghagen NSM; Venter JC, Complete genome sequence of the methanogenic
archaeon, Methanococcus. Science 273,
pages 1058‑1073, 1996
26. Selkov
E; Galimova M; Goryanin 1; Gretchkin Y; lvanova N; Komarov Y; Maltsev N;
Mikhailova N; Nenashev V; Overbeek R; Panyushkina E; Pronevitch L; Selkov E Jr,
The metabolic pathway collection: an update, Nucleic Acids Res. 25, pages 37‑38. 1997
27. Maidak
BL; Olsen GJ; Larsen N; Overbeek R; McCaughey MJ; Woese CR, The RDP (Ribosomal
Database Project). Nucleic Acids Res. 25, pages 109‑111, 1997
28. Overbeek
R; Laxsen N; Smith W; Maltsev N; Selkov E, Representation of function: the next
step, Gene 191, pages GC1‑GC9,1997
29. Selkov
E; Maltsev N; Olsen GJ; Overbeek R; Whitman WB, A reconstruction of the
metabolism of Methanococcus jannaschii from sequence data, Gene 197, pages GC11‑G26,1997
30. Dsouza
M; Laxsen N; Overbeek R, Searching for patterns in genomic data Trends
Genet. 13, pages 497‑498, 1997
31. Deckert
G; Warren PV; Gaasterland T; Young WG; Lenox AL; Graham DE; Overbeek R; Snead
MA; Keller M; Aujay M; Huber R; Feldman RA; Short JM; Olsen GJ; Swanson RV, The
complete genome of the hyperthermophilic bacterium Aquifex a,eolicus, Nature
392, pages 353‑358, 1998
32. Maidak
BL; Cole JR; Parker CT Jr; Garrity GM; Larsen N; Li B; Lilburn TG; McCaughey
MJ; Olsen GJ; Overbeek R; Pramanik S; Schmidt TM; Tiedje JM; Woese CR, A new
version of the RDP (Ribosomal Database Project), Nucleic Acids Res. Jan
1;27(l), pages 171‑173., 1999
33. Overbeek
R; Fonstein M; D'Souza M; Pusch GD; Maltsev N, The use of gene clusters to
infer functional coupling, Proc Natl Acad Sci USA 96, pages 2896‑2901, 1999
Technical Reports
1. Lusk,
Ewing L. and Ross A. Overbeek, An LMA‑Based Theorem Prover, Technical
Report ANL‑82‑75, Argonne
National Laboratory, December 1982.
2.
Lusk, Ewing L. and Ross
A. Overbeek, An Approach to Programming Multiprocessing Algorithms on the
Denelcor HEP, Technical Report ANL‑83‑96, Argonne National Laboratory, December 1983.
3.
Lusk, Ewing L. and Ross
A. Overbeek, Implementation of Monitors with Macros: A Programming Aid for
the HEP and Other Parallel Processors, Technical Report ANL‑83‑97, Argonne National Laboratory, December 1983.
4. Lusk,
Ewing L. and Ross A. Overbeek, Logic Machine Architecture Inference
Mechanisms ‑ Layer 2 User Reference Manual ‑ Release 2.0, Technical
Report ANL‑82‑84, Argonne
National Laboratory, April 1984.
5. Lusk,
Ewing L. and Ross A. Overbeek, The Automated Reasoning System ITP, Technical
Report ANL‑84‑27, Argonne
National Laboratory, April 1984.
6. Lusk,
Ewing L. and Ross A. Overbeek, Implementing Multiprocessing Algorithms Now, New
Directions in Software for Advanced Computer Architectures, Technical Report
ANLIMCS‑TM‑32, pp. 5‑10, MCS, Argonne National Laboratory, August 1984.
7. Lusk,
Ewing L. and Ross A. Overbeek, Parallelism in Automated Reasoning Systems, New
Directions in Software for Advanced Computer Architectures, Technical Report
ANLIMCS‑TM‑32, pp. 25‑34,
MCS, Argonne National Laboratory, August 1984.
8. Lusk,
Ewing L. and Ross A. Overbeek, Stalking the Gigalip, New Directions in
Software for Advanced Computer Architectures, Technical Report ANLIMCS‑TM‑32,
pp. 15‑24, MCS, Argonne
National Laboratory, August 1984.
9. Clausing,
J., R. Hagstrom, E. Lusk, and R. A. Overbeek, Use of Monitors in Pascal on the
Lemur: A Tutorial on the Barrier, Self‑Scheduling DO‑Loop, and
Askfor Monitors, Technical Report ANL‑84‑53, Argonne National Laboratory, July 1984.
10. Lusk,
Ewing L. and Ross A. Overbeek, Research Topics: Multiprocessing Algorithms
for Computational Logic, Technical Report ANLIMCS‑TM‑31, MCS, Argonne National Laboratory, July 1984.
11. Gabriel,
J., T. Lindholm, E. Lusk, and R. A. Overbeek, A Tutorial on the Warren
Abstract Machine, Technical Report ANL‑84‑84, Argonne National Laboratory, Argonne, Illinois,
October 1984.
12. Gabriel,
J., T. Lindholm, E. Lusk, and R. A. Overbeek, A Short Note on Achievable LIP
rates Using the Warren Abstract Prolog Machine, Technical Report ANLIMCSTM‑36,
MCS, Argonne National Laboratory,
September 1984.
13. Lusk,
E. L., R. L. Stevens, and R. A. Overbeek, A Tutorial on the Use of Monitors
in C. Writing Portable Code for Multiprocessors, Technical Report ANL‑85‑2,
Argonne National Laboratory, January
1985.
14. Lusk,
E. L., R. A. Overbeek, and B. Parrello, Designing IMS Data Bases from Entity‑Relationship
Models, Auerbach Publishers, Inc.,
1985.
15. Butler,
M., E. Lusk, W. McCune, and R. Overbeek, Parallel Logic Programming for
Numeric Applications, Technical Report ANLIMCS‑ TM‑ 72, MCS, Argonne National Laboratory, November 1985.
16. Glickfeld,
B. and R. Overbeek, Quasi‑Automatic Parallelization: A Simplied
Approach to Multiprocessing, Technical Report ANL‑855‑70, Argonne National Laboratory, October 1985.
17. Glickfeld,
B. and R. Overbeek, An Approach to Implementing State Space Searches on
Heterogeneous Systems of Multiprocessors, Technical Report ANL‑87‑36,
Argonne National Laboratory,
September 1987.
18. Carlsson,
M., K. Danhof, and R. Overbeek, Practical Issues Relating to the Internal
Database Predicates in an OR‑Parallel Prolog: Extensions and Useful
Hacks, Technical Report ANL‑88‑11, Argonne National Laboratory, February 1988.
19. Butler,
R., T. Butler, I. Foster, N. Karonis, R. Olson, R. Overbeek, N. Pfluger, M.
Price, and S. Tuecke, Generating Alignments of Genetic Sequences, Technical
Report ANLIMCS‑TM‑132,, Argonne
National Laboratory, June 1989.
20. Jindal,
A., R. Overbeek, and W. McCune, A Parallel Processing Approach for
Implementing High‑Performance First‑Order Logic Dedeuction Systems,
Technical Report ANLIMCS‑TM‑131,, Argonne National Laboratory, April 1989.
21. Singh,
A. K. and R. Overbeek Derivation of Efficient Parallel Programs: an Example
from Genetic Sequence Analysis, Technical Report ANLIMCS‑P104‑0989,
Argonne National Laboratory, 1989.
22. Winker,
S., R. Overbeek, C. R. Woese, G. J. Olsen, and N. Pfluger An Automated
Procedure for Covariation‑based Detection of RNA Structure, Technical
Report ANL89142, Argonne National
Laboratory, 1989
23. Foster,
I. and R. Overbeek Bilingual Parallel Programming, Technical Report ANLIMCS‑P163‑0790,
, Argonne National Laboratory, 1990
24. Baehr,
A., R. Hagstrom, D. Joerg, and R. Overbeek, Querying Genomic Databases,
Technical Report ANLIMCS‑TM‑155,, Argonne National Laboratory, September 1991.
25. Baehr,
A., G. Dunham, A. Ginsburg, R. Hagstrom, D. Joerg, T. Kazic, H. Matsuda, G.
Michaels, R. Overbeek, K. E. Rudd, C. Smith, R. Taylor, K. Yoshida, and D.
Zawada, An Integrated Database to Support Research on Escherichia coli Report ANL‑92/1 Argonne National Laboratory,
January 1992.
26. Hagstrom,
R., G. S. Michaels, R. Overbeek, M. Price, R. Taylor, K. Yoshida, and D.
Zawada, GenoGraphics for Open Windows, Technical Report ANL‑92111,, Argonne National Laboratory, April 1992.
27. Hagstrom,
J. N., R. Hagstrom, R. Overbeek, M. Price, and L. Schrage, Maximum
Likelihood Genetic Sequence Reconstruction from Oligo Content, Technical Report
ANLIMCS‑P309‑0592,, Argonne
National Laboratory, September 1992.
28. Hagstrom,
R., G. S. Michaels, R. Overbeek, M. Price, and R. Taylor, Overview of the
Integrated Genomic Data System (IGD), Techical Report ANLIMCSP325‑0992,, Argonne National Laboratory, October 1992.
29. Overbeek,
R. and M. Price, Accessing Integrated Genomic Data Using GenoBase: A
Tutorial (Part 1), Report ANLIMCS‑TM‑173,, Argon ne National Laboratory, January, 1993
30. Lusk,
E. L., S. Mudambi, R. Overbeek, and P. Szeredi Applications of the Aurora
Parallel Prolog System to Computational Molecular Biology Report ANLIMCS‑P372‑0793,
Argonne National Laboratory, July
1993
Other Publications
1. Overbeek,
R., A new class of automated theorem‑proving algorithms, Ph.D. thesis,
Penn. State Univ., 1971.
2. Overbeek,
R., The representation of many‑one degrees by decision problems of Turing
machines, The Journal of Symbolic Logic, 36, p. 706, 1971. (abstract)
3. Overbeek,
R., The representation of many‑one degrees by the word problem for Thue
Systems, The Journal of Symbolic Logic, 36, p. 584, 1971. (abstract)
4. Lusk,
E., R. Overbeek, and B. Parrello, A practical design methodology for the
implementation of IMS databases, using the entity‑ relationship model, Proceedings
of the ACM‑SIGMOD, May 1980.
5. Henschen,
L., E. Lusk, R. Overbeek, B. Smith, R. Veroff, S. Winker, and L. Wos, Challenge
Problem 1, SIGART Newsletter, no. 72, pp. 30‑31, July 1980.
31. Olsen,
G. J., R. overbeek, N. Larsen, and C. R. Woese, The Ribosomal Database Project:
Updated Description Nucleic Acids Res. 19, (1991) 4817
32. Overbeek,
R. and I. Foster, Aligning Multiple RNA Sequences Automated Reasoning:
Essays in Honor of Woody Bledsoe, pp. 231‑248,
ed. Robert S. Boyer, Kluwer Academic Pub., 1991
33. Michaels,
G. S., R. Taylor, P. Munson, R. Hagstrom, M. Price, and R. Overbeek Searching
for Genomic Organizational Motifs: Explorations of the E.coli Chromosome Computers
in Chemistry (in press, 1992)
34. Olsen,
G. J., H. Matsuda, R. Hagstrom, and R. Overbeek, fastDNAml: a tool for
construction of phylogenetic trees of DNA sequences using maximum likelihood CABIOS,
1993
35. Larsen,
N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L.
Marsh, and C. R. Woese, The Ribosomal Database Project Nucleic Acids Res. 21, (1993) 3021‑3023
36. Olsen,
G. J., C. R. Woese, and R. Overbeek, The Winds of (Evolutionary) Change:
Breathing New Life into Microbiology Journal of Bacteriology, Jan 1994, pp.1‑6
37. Hagstrom,
J. N., R. Hagstrom, R. Overbeek, M. Price, and L. Schrage, Maximum
Likelihood Genetic Sequence Reconstruction from Oligo Networks, Volume 24, pp. 297‑302,, August 1994.
38. Smith,
S.W., R. Overbeek, C. R. Woese, W. Gilbert, and P. M. Gillevet, The Genetic
Data ERnvironment, an Expandable GUIJor Multiple Sequence Analysis, CABIOS, 10, 671‑675, 1994
39. Kagawa,
H. K., J. Osipiuk, N. Maltsev, R. Overbeek, E. Qualte-Randall, A. Joachimiak,
and J. D. Trent The 60 kDa Heat
Shock Proteins in the Hyperthermophilic Archaeon Sulfolobus shibatae, Journal
of Molecular Biology, 253, 712‑725,
1995
40. Selkov,
E., S. Basmanova, I. Goryanin, Y. Gretchkin, T. Gaasterland, N. Maltsev, V.
Nenashev, R. Overbeek, E. Panyushkina, L. Pronevitch, E. Selkov Jr., and I.
Yunus, The Metabolic Pathway Collection from EMP: the Enzymes and Metabolic
Pathways Database, Journal of Nucleic Acids Research, Vol. 24, 1, 26‑28, January, 1996
41. B.L.
Maidak, G.J. Olsen, N. Larsen, R. Overbeek, M.J. McCaughey, and C.R. Woese The
Ribosomal Database Project (RDP), Journal of Nucleic Acids Research, Vol. 24, 1, 82‑85, January, 1996