Ross A. Overbeek

Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross A. Overbeek: Real Time Metagenomics: Using k-mers to annotate metagenomes. Bioinformatics 28(24): 3316-3317 (2012)

Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards: Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 11: 319 (2010)

Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens: The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Research 35(Database-Issue): 347-353 (2007)

Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik: Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) 2005: 478-486

Ross A. Overbeek, Terry Disz, Rick L. Stevens: The SEED: a peer-to-peer environment for genome annotation. Commun. ACM 47(11): 46-51 (2004)

Alexei E. Kazakov, Olga Vassieva, Mikhail S. Gelfand, Andrei Osterman, Ross A. Overbeek: Bioinformatics classification and functional analysis of PhoH homologs. In Silico Biology 3: 2 (2003)

Ross A. Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon D. Pusch, Evgeni Selkov Jr., Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vassieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, Nikos Kyrpides: The ERGOTM genome analysis and discovery system. Nucleic Acids Research 31(1): 164-171 (2003)

Ross A. Overbeek, Niels Larsen, Gordon D. Pusch, Mark D'Souza, Evgeni Selkov Jr., Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, Evgeni Selkov: WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Research 28(1): 123-125 (2000)

Bonnie L. Maidak, James R. Cole, Charles T. Parker Jr., George M. Garrity, Niels Larsen, Bing Li, Timothy G. Lilburn, Michael J. McCaughey, Gary J. Olsen, Ross A. Overbeek, Sakti Pramanik, Thomas M. Schmidt, James M. Tiedje, Carl R. Woese: A new version of the RDP (Ribosomal Database Project). Nucleic Acids Research 27(1): 171-173 (1999)

Ross A. Overbeek, Michael Fonstein, Mark D'Souza, Gordon D. Pusch, Natalia Maltsev: Use of contiguity on the chromosome to predict functional coupling. In Silico Biology 1: 9 (1998)

Barry Zeeberg, Kevin Watanabe, Susumu Goto, Ross A. Overbeek, Larry Kerschberg, George Michaels: Metabolic Pathway Interface to Molecular Biology Databases. SSDBM 1998: 238-241

Evgeni Selkov, Miliusha Galimova, Igor Goryanin, Yuri Grechkin, Natalia Ivanova, Yuri Komarov, Natalia Maltsev, Natalia Mikhailova, Valeri Nenashev, Ross A. Overbeek, Elena Panyushkina, Lyudmila Pronevitch, Evgeni Selkov Jr.: The metabolic pathway collection: an update. Nucleic Acids Research 25(1): 37-38 (1997)

Bonnie L. Maidak, Gary J. Olsen, Niels Larsen, Ross A. Overbeek, Michael J. McCaughey, Carl R. Woese: The RDP (Ribosomal Database Project). Nucleic Acids Research 25(1): 109-111 (1997)

Evgeni Selkov, Svetlana Basmanova, Terry Gaasterland, Igor Goryanin, Yuri Grechkin, Natalia Maltsev, Valeri Nenashev, Ross A. Overbeek, Elena Panyushkina, Lyudmila Pronevitch, Evgeni Selkov Jr., Ilya Yunus: The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Research 24(1): 26-28 (1996)

Bonnie L. Maidak, Gary J. Olsen, Niels Larsen, Ross A. Overbeek, Michael J. McCaughey, Carl R. Woese: The Ribosomal Database Project (RDP). Nucleic Acids Research 24(1): 82-85 (1996)

Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross A. Overbeek: fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Computer Applications in the Biosciences 10(1): 41-48 (1994)

Steven W. Smith, Ross A. Overbeek, Carl R. Woese, W. Gilbert, P. M. Gillevet: The genetic data environment an expandable GUI for multiple sequence analysis. Computer Applications in the Biosciences 10(6): 671-675 (1994)

Ralph Butler, Ross A. Overbeek: Formula Databases for High-Performance Resolution/Paramodulation Systems. J. Autom. Reasoning 12(2): 139-156 (1994)

Jane N. Hagstrom, Ray Hagstrom, Ross A. Overbeek, Morgan Price, Linus Schrage: Maximum likelihood genetic sequence reconstruction from oligo content. Networks 24(5): 297-302 (1994)

Hideo Matsuda, Gary J. Olsen, Ross A. Overbeek, Yukio Kaneda: Fast phylogenetic analysis on a massively parallel machine. International Conference on Supercomputing 1994: 297-302

George S. Michaels, Ronald Taylor, Ray Hagstrom, Morgan Price, Ross A. Overbeek: Searching for Genomic Organizational Motifs: Explorations of the Escherichia Coli Chromosome. Computers & Chemistry 17(2): 209-217 (1993)

Ross A. Overbeek: The CADE-11 Competitions: A Personal View. J. Autom. Reasoning 11(3): 315-316 (1993)

Niels Larsen, Gary J. Olsen, Bonnie L. Maidak, Michael J. McCaughey, Ross A. Overbeek, Thomas J. Macke, Terry L. Marsh, Carl R. Woese: The ribosomal database project. Nucleic Acids Research 21(13): 3021-3023 (1993)

Ewing L. Lusk, Shyam Mudambi, Ross A. Overbeek, Péter Szeredi: Applications of the Aurora Parallel Prolog System to Computational Molecular Biology. ILPS 1993: 353-369

Anita Jindal, Ross A. Overbeek, Waldo C. Kabat: Exploitation of Parallel Processing for Implementing High-Performance Deduction Systems. J. Autom. Reasoning 8(1): 23-38 (1992)

Ross A. Overbeek: The Role of Logic Programming in the 21st Century - Panel Position Paper. FGCS 1992: 223-224

Kaoru Yoshida, Cassandra Smith, Toni Kazic, George Michaels, Ronald Taylor, David Zawada, Ray Hagstrom, Ross A. Overbeek: Toward a Human Genome Encyclopedia. FGCS 1992: 307-320

Ewing L. Lusk, Ross A. Overbeek, Shyam Mudambi, Péter Szeredi: Applications of the Aurora Parallel Prolog System to Computational Molecular Biology. IJCSLP Workshop on Concurrent and Parallel Implementations 1992

Ross A. Overbeek: Logic Programming and Genetic Sequence Analysis: a Tutorial. JICSLP 1992: 32-34

Larry Wos, Ross A. Overbeek, Ewing L. Lusk: Subsumption, a Sometimes Undervalued Procedure. Computational Logic - Essays in Honor of Alan Robinson 1991: 3-40

Ross A. Overbeek, Ian T. Foster: Aligning Multiple RNA Sequences. Automated Reasoning: Essays in Honor of Woody Bledsoe 1991: 231-248

S. Winker, Ross A. Overbeek, Carl R. Woese, Gary J. Olsen, N. Pfluger: Structure detection through automated covariance search. Computer Applications in the Biosciences 6(4): 365-371 (1990)

Ewing L. Lusk, Ralph Butler, Terrence Disz, Robert Olson, Ross A. Overbeek, Rick Stevens, David H. D. Warren, Alan Calderwood, Péter Szeredi, Seif Haridi: The Aurora or-parallel Prolog system. New Generation Comput. 7(2-3): 243-271 (1990)

Larry Wos, S. Winker, William McCune, Ross A. Overbeek, Ewing L. Lusk, Rick L. Stevens, Ralph Butler: Automated Reasoning Contributed to Mathematics and Logic. CADE 1990: 485-499

Ralph Butler, Ian T. Foster, Anita Jindal, Ross A. Overbeek: A High-Performance Parallel Theorem Prover. CADE 1990: 649-650

Ambuj K. Singh, Ross A. Overbeek: Derivation of efficient parallel programs: An example from genetic sequence analysis. International Journal of Parallel Programming 18(6): 447-484 (1989)

Barney Glickfeld, Ross A. Overbeek: Geometric specification of scheduling constraints: A simplified approach to multiprocessing. Parallel Computing 6(3): 325-337 (1988)

Ewing L. Lusk, Ralph Butler, Terry Disz, Robert Olson, Ross A. Overbeek, Rick L. Stevens, David H. D. Warren, Alan Calderwood, Péter Szeredi, Seif Haridi, Per Brand, Mats Carlsson, Andrzej Ciepielewski, Bogumil Hausman: The Aurora Or-Parallel Prolog System. FGCS 1988: 819-830

Mats Carlsson, Kenneth J. Danhof, Ross A. Overbeek: A Simplified Approach to the Implementation of AND-Parallelism in an OR-Parallel Environment. ICLP/SLP 1988: 1565-1577

Ralph Butler, Terry Disz, Ewing L. Lusk, Robert Olson, Ross A. Overbeek, Rick L. Stevens: Scheduling OR-Parallelism: An Argonne Perspective. ICLP/SLP 1988: 1590-1605

Ewing L. Lusk, Ross A. Overbeek (Eds.): 9th International Conference on Automated Deduction, Argonne, Illinois, USA, May 23-26, 1988, Proceedings. Lecture Notes in Computer Science 310, Springer 1988, isbn 3-540-19343-X

Terry Disz, Ewing L. Lusk, Ross A. Overbeek: Experiments with OR-Parallel Logic Programs. ICLP 1987: 576-600

Robert S. Boyer, Ewing L. Lusk, William McCune, Ross A. Overbeek, Mark E. Stickel, Larry Wos: Set Theory in First-Order Logic: Clauses for Gödel's Axioms. J. Autom. Reasoning 2(3): 287-327 (1986)

Barney Glickfeld, Ross A. Overbeek: A Foray Into Combinatory Logic. J. Autom. Reasoning 2(4): 419-431 (1986)

Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek: Paths to High-Performance Automated Theorem Proving. CADE 1986: 588-597

Ewing L. Lusk, William McCune, Ross A. Overbeek: ITP at Argonne National Laboratory. CADE 1986: 697-698

Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek: Parallel Logic Programming for Numeric Applications. ICLP 1986: 375-388

Bruce D. Parrello, Ross A. Overbeek, Ewing L. Lusk: The Design of Entity-Relationship Models for General Ledger Systems. Data Knowl. Eng. 1(2): 155-180 (1985)

Ewing L. Lusk, Ross A. Overbeek: Non-Horn Problems. J. Autom. Reasoning 1(1): 103-114 (1985)

Ewing L. Lusk, Ross A. Overbeek: Reasoning about Equality. J. Autom. Reasoning 1(2): 209-228 (1985)

Bradley J. Lucier, Ross A. Overbeek: A parallel adaptive numerical scheme for hyperbolic systems for conservation laws. PPSC 1985: 203-219

Ewing L. Lusk, Ross A. Overbeek: A Portable Environment for Research in Automated Reasoning. CADE 1984: 43-52

G. Margrave, Ewing L. Lusk, Ross A. Overbeek: Tools for the Creation of IMS Database Designs from Entity-Relationship Diagrams. ER 1983: 501-515

Paul K. Blackwell, Dan Kapp, Ross A. Overbeek, H. J. Spencer, Gio Wiederhold, Stanley B. Zdonik: Data Management: A Practical View (Panel). ER 1983: 809

Ewing L. Lusk, William McCune, Ross A. Overbeek: Logic Machine Architecture: Kernel Funtions. CADE 1982: 70-84

Ewing L. Lusk, William McCune, Ross A. Overbeek: Logic Machine Architecture: Inference Mechanisms. CADE 1982: 85-108

Ewing L. Lusk, Gene Petrie, Ross A. Overbeek: Item Tracking Entity-Relationship Models. ER 1981: 213-233

Larry Wos, Ross A. Overbeek, Lawrence J. Henschen: Hyperparamodulation: A Refinement of Paramodulation. CADE 1980: 208-219

Ross A. Overbeek, Ewing L. Lusk: Data Structures and Control Architectures for Implementation of Theorem-Proving Programs. CADE 1980: 232-249

Ewing L. Lusk, Ross A. Overbeek, Bruce D. Parrello: A Practical Design Methodology for the Implementation of IMS Databases, Using the Entity-Relationship Model. SIGMOD Conference 1980: 9-21

Ewing L. Lusk, Ross A. Overbeek: A DML for Entity-Relationship Models. ER 1979: 445-462

John D. McCharen, Ross A. Overbeek, Larry Wos: Problems and Experiments for and with Automated Theorem-Proving Programs. IEEE Trans. Computers 25(8): 773-782 (1976)

Lawrence J. Henschen, Ross A. Overbeek, Larry Wos: A Theorem-Proving Language for Experimentation. Commun. ACM 17(6): 308-314 (1974)

Ross A. Overbeek: A New Class of Automated Theorem-Proving Algorithms. J. ACM 21(2): 191-200 (1974)