Ross A. Overbeek

75 papers A 15B 3Misc 1Journal 41Unranked 14

Year	Rank	Type	Title / Venue / Authors
2020	J	`jnl`	The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 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
2019	J	`jnl`	A machine learning-based service for estimating quality of genomes using PATRIC. BMC Bioinform. Bruce D. Parrello, Rory Butler, Philippe Chlenski, Robert Olson, Jamie C. Overbeek, Gordon D. Pusch, Veronika Vonstein, Ross A. Overbeek
2019	J	`jnl`	PATRIC as a unique resource for studying antimicrobial resistance. Briefings Bioinform. 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
2017	J	`jnl`	Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 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
2015	Misc	`ed.`	9th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2015, 3-5 June, 2015, Salamanca, Spain. PACBB Ross A. Overbeek, Miguel P. Rocha, Florentino Fdez-Riverola, Juan Francisco de Paz
2014	J	`jnl`	Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings Bioinform. José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry
2014	J	`jnl`	PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 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
2014	J	`jnl`	The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 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
2012	J	`jnl`	Real Time Metagenomics: Using Bioinform. Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross A. Overbeek
2010	J	`jnl`	Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinform. Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards
2007	J	`jnl`	The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 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
2005	—	`conf`	Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik
2005	—	`conf`	Challenges in large scale distributed computing: bioinformatics. CLADE Terry Disz, Michael Kubal, Robert Olson, Ross A. Overbeek, Rick L. Stevens
2004	J	`jnl`	The SEED: a peer-to-peer environment for genome annotation. Commun. ACM Ross A. Overbeek, Terry Disz, Rick L. Stevens
2003	J	`jnl`	Bioinformatics classification and functional analysis of PhoH homologs. Silico Biol. Alexei E. Kazakov, Olga Vassieva, Mikhail S. Gelfand, Andrei Osterman, Ross A. Overbeek
2003	J	`jnl`	The ERGOTM genome analysis and discovery system. Nucleic Acids Res. 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
2000	J	`jnl`	WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. Ross A. Overbeek, Niels Larsen, Gordon D. Pusch, Mark D'Souza, Evgeni Selkov Jr., Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, Evgeni Selkov
1999	J	`jnl`	A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 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
1998	B	`conf`	Metabolic Pathway Interface to Molecular Biology Databases. SSDBM Barry Zeeberg, Kevin Watanabe, Susumu Goto, Ross A. Overbeek, Larry Kerschberg, George Michaels
1998	J	`jnl`	Use of contiguity on the chromosome to predict functional coupling. Silico Biol. Ross A. Overbeek, Michael Fonstein, Mark D'Souza, Gordon D. Pusch, Natalia Maltsev
1997	J	`jnl`	The RDP (Ribosomal Database Project). Nucleic Acids Res. Bonnie L. Maidak, Gary J. Olsen, Niels Larsen, Ross A. Overbeek, Michael J. McCaughey, Carl R. Woese
1997	J	`jnl`	The metabolic pathway collection: an update. Nucleic Acids Res. 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.
1996	J	`jnl`	The Ribosomal Database Project (RDP). Nucleic Acids Res. Bonnie L. Maidak, Gary J. Olsen, Niels Larsen, Ross A. Overbeek, Michael J. McCaughey, Carl R. Woese
1996	J	`jnl`	The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Res. 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
1994	A	`conf`	Fast phylogenetic analysis on a massively parallel machine. International Conference on Supercomputing Hideo Matsuda, Gary J. Olsen, Ross A. Overbeek, Yukio Kaneda
1994	J	`jnl`	Formula Databases for High-Performance Resolution/Paramodulation Systems. J. Autom. Reason. Ralph Butler, Ross A. Overbeek
1994	J	`jnl`	Maximum likelihood genetic sequence reconstruction from oligo content. Networks Jane N. Hagstrom, Ray Hagstrom, Ross A. Overbeek, Morgan Price, Linus Schrage
1994	J	`jnl`	The genetic data environment an expandable GUI for multiple sequence analysis. Comput. Appl. Biosci. Steven W. Smith, Ross A. Overbeek, Carl R. Woese, W. Gilbert, P. M. Gillevet
1994	J	`jnl`	fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross A. Overbeek
1993	—	`conf`	Applications of the Aurora Parallel Prolog System to Computational Molecular Biology. ILPS Ewing L. Lusk, Shyam Mudambi, Ross A. Overbeek, Péter Szeredi
1993	J	`jnl`	Searching for Genomic Organizational Motifs: Explorations of the Escherichia Coli Chromosome. Comput. Chem. George S. Michaels, Ronald C. Taylor, Ray Hagstrom, Morgan Price, Ross A. Overbeek
1993	J	`jnl`	The CADE-11 Competitions: A Personal View. J. Autom. Reason. Ross A. Overbeek
1993	J	`jnl`	The ribosomal database project. Nucleic Acids Res. Niels Larsen, Gary J. Olsen, Bonnie L. Maidak, Michael J. McCaughey, Ross A. Overbeek, Thomas J. Macke, Terry L. Marsh, Carl R. Woese
1992	—	`conf`	Applications of the Aurora Parallel Prolog System to Computational Molecular Biology. IJCSLP Workshop on Concurrent and Parallel Implementations Ewing L. Lusk, Ross A. Overbeek, Shyam Mudambi, Péter Szeredi
1992	J	`jnl`	Exploitation of Parallel Processing for Implementing High-Performance Deduction Systems. J. Autom. Reason. Anita Jindal, Ross A. Overbeek, Waldo C. Kabat
1992	—	`conf`	Logic Programming and Genetic Sequence Analysis: a Tutorial. JICSLP Ross A. Overbeek
1992	—	`conf`	The Role of Logic Programming in the 21st Century - Panel Position Paper. FGCS Ross A. Overbeek
1992	—	`conf`	Toward a Human Genome Encyclopedia. FGCS Kaoru Yoshida, Cassandra Smith, Toni Kazic, George Michaels, Ronald C. Taylor, David Zawada, Ray Hagstrom, Ross A. Overbeek
1991	—	`conf`	Aligning Multiple RNA Sequences. Automated Reasoning: Essays in Honor of Woody Bledsoe Ross A. Overbeek, Ian T. Foster
1991	—	`conf`	Subsumption, a Sometimes Undervalued Procedure. Computational Logic - Essays in Honor of Alan Robinson Larry Wos, Ross A. Overbeek, Ewing L. Lusk
1990	A	`conf`	A High-Performance Parallel Theorem Prover. CADE Ralph Butler, Ian T. Foster, Anita Jindal, Ross A. Overbeek
1990	A	`conf`	Automated Reasoning Contributed to Mathematics and Logic. CADE Larry Wos, Steve Winker, William McCune, Ross A. Overbeek, Ewing L. Lusk, Rick L. Stevens, Ralph Butler
1990	J	`jnl`	Structure detection through automated covariance search. Comput. Appl. Biosci. Steve Winker, Ross A. Overbeek, Carl R. Woese, Gary J. Olsen, N. Pfluger
1990	J	`jnl`	The Aurora or-parallel Prolog system. New Gener. Comput. Ewing L. Lusk, Ralph Butler, Terrence Disz, Robert Olson, Ross A. Overbeek, Rick Stevens, David H. D. Warren, Alan Calderwood, Péter Szeredi, Seif Haridi
1989	J	`jnl`	Derivation of efficient parallel programs: An example from genetic sequence analysis. Int. J. Parallel Program. Ambuj K. Singh, Ross A. Overbeek
1989	—	`ed.`	Logic Programming, Proceedings of the North American Conference 1989, Cleveland, Ohio, USA, October 16-20, 1989. 2 Volumes NACLP Ewing L. Lusk, Ross A. Overbeek
1988	A	`ed.`	9th International Conference on Automated Deduction, Argonne, Illinois, USA, May 23-26, 1988, Proceedings CADE Ewing L. Lusk, Ross A. Overbeek
1988	—	`conf`	A Simplified Approach to the Implementation of AND-Parallelism in an OR-Parallel Environment. ICLP/SLP Mats Carlsson, Kenneth J. Danhof, Ross A. Overbeek
1988	J	`jnl`	Geometric specification of scheduling constraints: A simplified approach to multiprocessing. Parallel Comput. Barney Glickfeld, Ross A. Overbeek
1988	—	`conf`	Scheduling OR-Parallelism: An Argonne Perspective. ICLP/SLP Ralph Butler, Terry Disz, Ewing L. Lusk, Robert Olson, Ross A. Overbeek, Rick L. Stevens
1988	—	`conf`	The Aurora Or-Parallel Prolog System. FGCS 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
1987	B	`conf`	Experiments with OR-Parallel Logic Programs. ICLP Terry Disz, Ewing L. Lusk, Ross A. Overbeek
1986	J	`jnl`	A Foray Into Combinatory Logic. J. Autom. Reason. Barney Glickfeld, Ross A. Overbeek
1986	A	`conf`	ITP at Argonne National Laboratory. CADE Ewing L. Lusk, William McCune, Ross A. Overbeek
1986	B	`conf`	Parallel Logic Programming for Numeric Applications. ICLP Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek
1986	A	`conf`	Paths to High-Performance Automated Theorem Proving. CADE Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek
1986	J	`jnl`	Set Theory in First-Order Logic: Clauses for Gödel's Axioms. J. Autom. Reason. Robert S. Boyer, Ewing L. Lusk, William McCune, Ross A. Overbeek, Mark E. Stickel, Larry Wos
1985	—	`conf`	A parallel adaptive numerical scheme for hyperbolic systems for conservation laws. PP Bradley J. Lucier, Ross A. Overbeek
1985	J	`jnl`	A technique for achieving portability among multiprocessors: Implementation on the Lemur. Parallel Comput. J. A. Clausing, Ray Hagstrom, Ewing L. Lusk, Ross A. Overbeek
1985	J	`jnl`	Non-Horn Problems. J. Autom. Reason. Ewing L. Lusk, Ross A. Overbeek
1985	J	`jnl`	Reasoning about Equality. J. Autom. Reason. Ewing L. Lusk, Ross A. Overbeek
1985	J	`jnl`	The Design of Entity-Relationship Models for General Ledger Systems. Data Knowl. Eng. Bruce D. Parrello, Ross A. Overbeek, Ewing L. Lusk
1984	A	`conf`	A Portable Environment for Research in Automated Reasoning. CADE Ewing L. Lusk, Ross A. Overbeek
1983	A	`conf`	Data Management: A Practical View (Panel). ER Paul K. Blackwell, Dan Kapp, Ross A. Overbeek, H. J. Spencer, Gio Wiederhold, Stanley B. Zdonik
1983	A	`conf`	Tools for the Creation of IMS Database Designs from Entity-Relationship Diagrams. ER G. Margrave, Ewing L. Lusk, Ross A. Overbeek
1982	A	`conf`	Logic Machine Architecture: Inference Mechanisms. CADE Ewing L. Lusk, William McCune, Ross A. Overbeek
1982	A	`conf`	Logic Machine Architecture: Kernel Funtions. CADE Ewing L. Lusk, William McCune, Ross A. Overbeek
1981	A	`conf`	Item Tracking Entity-Relationship Models. ER Ewing L. Lusk, Gene Petrie, Ross A. Overbeek
1980	—	`conf`	A Practical Design Methodology for the Implementation of IMS Databases, Using the Entity-Relationship Model. SIGMOD Conference Ewing L. Lusk, Ross A. Overbeek, Bruce D. Parrello
1980	A	`conf`	Data Structures and Control Architectures for Implementation of Theorem-Proving Programs. CADE Ross A. Overbeek, Ewing L. Lusk
1980	A	`conf`	Hyperparamodulation: A Refinement of Paramodulation. CADE Larry Wos, Ross A. Overbeek, Lawrence J. Henschen
1979	A	`conf`	A DML for Entity-Relationship Models. ER Ewing L. Lusk, Ross A. Overbeek
1976	J	`jnl`	Problems and Experiments for and with Automated Theorem-Proving Programs. IEEE Trans. Computers John D. McCharen, Ross A. Overbeek, Larry Wos
1974	J	`jnl`	A New Class of Automated Theorem-Proving Algorithms. J. ACM Ross A. Overbeek
1974	J	`jnl`	A Theorem-Proving Language for Experimentation. Commun. ACM Lawrence J. Henschen, Ross A. Overbeek, Larry Wos