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Ross A. Overbeek
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- affiliation: University of Minnesota, USA
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2020 – today
- 2020
- [j41]James J. Davis, Alice R. Wattam, Ramy K. Aziz, Thomas S. Brettin, Ralph Butler, Rory Butler, Philippe Chlenski, Neal Conrad, Allan Dickerman, Emily M. Dietrich, Joseph L. Gabbard, Svetlana Gerdes, Andrew Guard, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Marcus Nguyen, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Jamie C. Overbeek, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Dawen Xie, Hyun Seung Yoo, Rick Stevens:
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 48(Database-Issue): D606-D612 (2020)
2010 – 2019
- 2019
- [j40]Dionysios A. Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas S. Brettin, Christopher Bun, Neal Conrad, James J. Davis, Emily M. Dietrich, Terry Disz, Svetlana Gerdes, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, John Santerre, Maulik Shukla, Rick L. Stevens, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo:
PATRIC as a unique resource for studying antimicrobial resistance. Briefings Bioinform. 20(4): 1094-1102 (2019) - [j39]Bruce D. Parrello, Rory Butler, Philippe Chlenski, Robert Olson, Jamie C. Overbeek, Gordon D. Pusch, Veronika Vonstein, Ross A. Overbeek:
A machine learning-based service for estimating quality of genomes using PATRIC. BMC Bioinform. 20(1): 486:1-486:9 (2019) - 2017
- [j38]Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas S. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyun Seung Yoo, Rick L. Stevens:
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 45(Database-Issue): D535-D542 (2017) - 2015
- [e3]Ross A. Overbeek, Miguel P. Rocha, Florentino Fdez-Riverola, Juan Francisco de Paz:
9th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2015, 3-5 June, 2015, Salamanca, Spain. Advances in Intelligent Systems and Computing 375, Springer 2015, ISBN 978-3-319-19775-3 [contents] - 2014
- [j37]José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry:
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings Bioinform. 15(4): 592-611 (2014) - [j36]Ross A. Overbeek, Robert Olson, Gordon D. Pusch, Gary J. Olsen, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Bruce D. Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam, Fangfang Xia, Rick Stevens:
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42(Database-Issue): 206-214 (2014) - [j35]Alice R. Wattam, David Abraham, Oral Dalay, Terry Disz, Timothy Driscoll, Joseph L. Gabbard, Joseph J. Gillespie, Roger Gough, Deborah Hix, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Robert Olson, Ross A. Overbeek, Gordon D. Pusch, Maulik Shukla, Julie Schulman, Rick L. Stevens, Daniel E. Sullivan, Veronika Vonstein, Andrew S. Warren, Rebecca Will, Meredith J. C. Wilson, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Bruno W. S. Sobral:
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 42(Database-Issue): 581-591 (2014) - 2012
- [j34]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. Bioinform. 28(24): 3316-3317 (2012) - 2010
- [j33]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 Bioinform. 11: 319 (2010)
2000 – 2009
- 2007
- [j32]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 Res. 35(Database-Issue): 347-353 (2007) - 2005
- [c31]Terry Disz, Michael Kubal, Robert Olson, Ross A. Overbeek, Rick L. Stevens:
Challenges in large scale distributed computing: bioinformatics. CLADE 2005: 57-65 - [c30]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 - 2004
- [j31]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) - 2003
- [j30]Alexei E. Kazakov, Olga Vassieva, Mikhail S. Gelfand, Andrei Osterman, Ross A. Overbeek:
Bioinformatics classification and functional analysis of PhoH homologs. Silico Biol. 3(1-2): 3-15 (2003) - [j29]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 Res. 31(1): 164-171 (2003) - 2000
- [j28]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 Res. 28(1): 123-125 (2000)
1990 – 1999
- 1999
- [j27]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 Res. 27(1): 171-173 (1999) - 1998
- [j26]Ross A. Overbeek, Michael Fonstein, Mark D'Souza, Gordon D. Pusch, Natalia Maltsev:
Use of contiguity on the chromosome to predict functional coupling. Silico Biol. 1(2): 93-108 (1998) - [c29]Barry Zeeberg, Kevin Watanabe, Susumu Goto, Ross A. Overbeek, Larry Kerschberg, George Michaels:
Metabolic Pathway Interface to Molecular Biology Databases. SSDBM 1998: 238-241 - 1997
- [j25]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 Res. 25(1): 37-38 (1997) - [j24]Bonnie L. Maidak, Gary J. Olsen, Niels Larsen, Ross A. Overbeek, Michael J. McCaughey, Carl R. Woese:
The RDP (Ribosomal Database Project). Nucleic Acids Res. 25(1): 109-111 (1997) - 1996
- [j23]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 Res. 24(1): 26-28 (1996) - [j22]Bonnie L. Maidak, Gary J. Olsen, Niels Larsen, Ross A. Overbeek, Michael J. McCaughey, Carl R. Woese:
The Ribosomal Database Project (RDP). Nucleic Acids Res. 24(1): 82-85 (1996) - 1994
- [j21]Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross A. Overbeek:
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10(1): 41-48 (1994) - [j20]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. Comput. Appl. Biosci. 10(6): 671-675 (1994) - [j19]Ralph Butler, Ross A. Overbeek:
Formula Databases for High-Performance Resolution/Paramodulation Systems. J. Autom. Reason. 12(2): 139-156 (1994) - [j18]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) - [c28]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 - 1993
- [j17]George S. Michaels, Ronald C. Taylor, Ray Hagstrom, Morgan Price, Ross A. Overbeek:
Searching for Genomic Organizational Motifs: Explorations of the Escherichia Coli Chromosome. Comput. Chem. 17(2): 209-217 (1993) - [j16]Ross A. Overbeek:
The CADE-11 Competitions: A Personal View. J. Autom. Reason. 11(3): 315-316 (1993) - [j15]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 Res. 21(13): 3021-3023 (1993) - [c27]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 - 1992
- [j14]Anita Jindal, Ross A. Overbeek, Waldo C. Kabat:
Exploitation of Parallel Processing for Implementing High-Performance Deduction Systems. J. Autom. Reason. 8(1): 23-38 (1992) - [c26]Ross A. Overbeek:
The Role of Logic Programming in the 21st Century - Panel Position Paper. FGCS 1992: 223-224 - [c25]Kaoru Yoshida, Cassandra Smith, Toni Kazic, George Michaels, Ronald C. Taylor, David Zawada, Ray Hagstrom, Ross A. Overbeek:
Toward a Human Genome Encyclopedia. FGCS 1992: 307-320 - [c24]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 - [c23]Ross A. Overbeek:
Logic Programming and Genetic Sequence Analysis: a Tutorial. JICSLP 1992: 32-34 - 1991
- [c22]Larry Wos, Ross A. Overbeek, Ewing L. Lusk:
Subsumption, a Sometimes Undervalued Procedure. Computational Logic - Essays in Honor of Alan Robinson 1991: 3-40 - [c21]Ross A. Overbeek, Ian T. Foster:
Aligning Multiple RNA Sequences. Automated Reasoning: Essays in Honor of Woody Bledsoe 1991: 231-248 - 1990
- [j13]Steve Winker, Ross A. Overbeek, Carl R. Woese, Gary J. Olsen, N. Pfluger:
Structure detection through automated covariance search. Comput. Appl. Biosci. 6(4): 365-371 (1990) - [j12]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 Gener. Comput. 7(2-3): 243-271 (1990) - [c20]Larry Wos, Steve 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 - [c19]Ralph Butler, Ian T. Foster, Anita Jindal, Ross A. Overbeek:
A High-Performance Parallel Theorem Prover. CADE 1990: 649-650
1980 – 1989
- 1989
- [j11]Ambuj K. Singh, Ross A. Overbeek:
Derivation of efficient parallel programs: An example from genetic sequence analysis. Int. J. Parallel Program. 18(6): 447-484 (1989) - [e2]Ewing L. Lusk, Ross A. Overbeek:
Logic Programming, Proceedings of the North American Conference 1989, Cleveland, Ohio, USA, October 16-20, 1989. 2 Volumes. MIT Press 1989, ISBN 0-262-62064-2 [contents] - 1988
- [j10]Barney Glickfeld, Ross A. Overbeek:
Geometric specification of scheduling constraints: A simplified approach to multiprocessing. Parallel Comput. 6(3): 325-337 (1988) - [c18]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 - [c17]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 - [c16]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 - [e1]Ewing L. Lusk, Ross A. Overbeek:
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 [contents] - 1987
- [c15]Terry Disz, Ewing L. Lusk, Ross A. Overbeek:
Experiments with OR-Parallel Logic Programs. ICLP 1987: 576-600 - 1986
- [j9]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. Reason. 2(3): 287-327 (1986) - [j8]Barney Glickfeld, Ross A. Overbeek:
A Foray Into Combinatory Logic. J. Autom. Reason. 2(4): 419-431 (1986) - [c14]Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek:
Paths to High-Performance Automated Theorem Proving. CADE 1986: 588-597 - [c13]Ewing L. Lusk, William McCune, Ross A. Overbeek:
ITP at Argonne National Laboratory. CADE 1986: 697-698 - [c12]Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek:
Parallel Logic Programming for Numeric Applications. ICLP 1986: 375-388 - 1985
- [j7]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) - [j6]Ewing L. Lusk, Ross A. Overbeek:
Non-Horn Problems. J. Autom. Reason. 1(1): 103-114 (1985) - [j5]Ewing L. Lusk, Ross A. Overbeek:
Reasoning about Equality. J. Autom. Reason. 1(2): 209-228 (1985) - [j4]J. A. Clausing, Ray Hagstrom, Ewing L. Lusk, Ross A. Overbeek:
A technique for achieving portability among multiprocessors: Implementation on the Lemur. Parallel Comput. 2(2): 137-162 (1985) - [c11]Bradley J. Lucier, Ross A. Overbeek:
A parallel adaptive numerical scheme for hyperbolic systems for conservation laws. PP 1985: 203-219 - 1984
- [c10]Ewing L. Lusk, Ross A. Overbeek:
A Portable Environment for Research in Automated Reasoning. CADE 1984: 43-52 - 1983
- [c9]G. Margrave, Ewing L. Lusk, Ross A. Overbeek:
Tools for the Creation of IMS Database Designs from Entity-Relationship Diagrams. ER 1983: 501-515 - [c8]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 - 1982
- [c7]Ewing L. Lusk, William McCune, Ross A. Overbeek:
Logic Machine Architecture: Kernel Funtions. CADE 1982: 70-84 - [c6]Ewing L. Lusk, William McCune, Ross A. Overbeek:
Logic Machine Architecture: Inference Mechanisms. CADE 1982: 85-108 - 1981
- [c5]Ewing L. Lusk, Gene Petrie, Ross A. Overbeek:
Item Tracking Entity-Relationship Models. ER 1981: 213-233 - 1980
- [c4]Larry Wos, Ross A. Overbeek, Lawrence J. Henschen:
Hyperparamodulation: A Refinement of Paramodulation. CADE 1980: 208-219 - [c3]Ross A. Overbeek, Ewing L. Lusk:
Data Structures and Control Architectures for Implementation of Theorem-Proving Programs. CADE 1980: 232-249 - [c2]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
1970 – 1979
- 1979
- [c1]Ewing L. Lusk, Ross A. Overbeek:
A DML for Entity-Relationship Models. ER 1979: 445-462 - 1976
- [j3]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) - 1974
- [j2]Lawrence J. Henschen, Ross A. Overbeek, Larry Wos:
A Theorem-Proving Language for Experimentation. Commun. ACM 17(6): 308-314 (1974) - [j1]Ross A. Overbeek:
A New Class of Automated Theorem-Proving Algorithms. J. ACM 21(2): 191-200 (1974)
Coauthor Index
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