Ross A. Overbeek

Publication Activity (10 Years)

Years Active: 1974-2020
Publications (10 Years): 4

Top Topics

Machine Learning

Technological Advances

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

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) (2020)
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) (2019)
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) (2019)
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) (2017)
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) (2014)
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) (2014)
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) (2014)
Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross A. Overbeek
-mers to annotate metagenomes. Bioinform. 28 (24) (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 Bioinform. 11 (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 Res. 35 (Database-Issue) (2007)
Terry Disz, Michael Kubal, Robert Olson, Ross A. Overbeek, Rick L. Stevens
Challenges in large scale distributed computing: bioinformatics. CLADE (2005)
Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik
Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) (2005)
Ross A. Overbeek, Terry Disz, Rick L. Stevens
The SEED: a peer-to-peer environment for genome annotation. Commun. ACM 47 (11) (2004)
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) (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 Res. 31 (1) (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 Res. 28 (1) (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 Res. 27 (1) (1999)
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) (1998)
Barry Zeeberg, Kevin Watanabe, Susumu Goto, Ross A. Overbeek, Larry Kerschberg, George Michaels
Metabolic Pathway Interface to Molecular Biology Databases. SSDBM (1998)
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) (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 Res. 25 (1) (1997)
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) (1996)
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) (1996)
Ralph Butler, Ross A. Overbeek
Formula Databases for High-Performance Resolution/Paramodulation Systems. J. Autom. Reason. 12 (2) (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. Comput. Appl. Biosci. 10 (6) (1994)
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) (1994)
Jane N. Hagstrom, Ray Hagstrom, Ross A. Overbeek, Morgan Price, Linus Schrage
Maximum likelihood genetic sequence reconstruction from oligo content. Networks 24 (5) (1994)
Hideo Matsuda, Gary J. Olsen, Ross A. Overbeek, Yukio Kaneda
Fast phylogenetic analysis on a massively parallel machine. International Conference on Supercomputing (1994)
Ross A. Overbeek
The CADE-11 Competitions: A Personal View. J. Autom. Reason. 11 (3) (1993)
George S. Michaels, Ronald Taylor, Ray Hagstrom, Morgan Price, Ross A. Overbeek
Searching for Genomic Organizational Motifs: Explorations of the Escherichia Coli Chromosome. Comput. Chem. 17 (2) (1993)
Ewing L. Lusk, Shyam Mudambi, Ross A. Overbeek, Péter Szeredi
Applications of the Aurora Parallel Prolog System to Computational Molecular Biology. ILPS (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 Res. 21 (13) (1993)
Kaoru Yoshida, Cassandra Smith, Toni Kazic, George Michaels, Ronald Taylor, David Zawada, Ray Hagstrom, Ross A. Overbeek
Toward a Human Genome Encyclopedia. FGCS (1992)
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
The Role of Logic Programming in the 21st Century - Panel Position Paper. FGCS (1992)
Ross A. Overbeek
Logic Programming and Genetic Sequence Analysis: a Tutorial. JICSLP (1992)
Anita Jindal, Ross A. Overbeek, Waldo C. Kabat
Exploitation of Parallel Processing for Implementing High-Performance Deduction Systems. J. Autom. Reason. 8 (1) (1992)
Larry Wos, Ross A. Overbeek, Ewing L. Lusk
Subsumption, a Sometimes Undervalued Procedure. Computational Logic - Essays in Honor of Alan Robinson (1991)
Ross A. Overbeek, Ian T. Foster
Aligning Multiple RNA Sequences. Automated Reasoning: Essays in Honor of Woody Bledsoe (1991)
Steve Winker, Ross A. Overbeek, Carl R. Woese, Gary J. Olsen, N. Pfluger
Structure detection through automated covariance search. Comput. Appl. Biosci. 6 (4) (1990)
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)
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) (1990)
Ralph Butler, Ian T. Foster, Anita Jindal, Ross A. Overbeek
A High-Performance Parallel Theorem Prover. CADE (1990)
Ambuj K. Singh, Ross A. Overbeek
Derivation of efficient parallel programs: An example from genetic sequence analysis. Int. J. Parallel Program. 18 (6) (1989)
Barney Glickfeld, Ross A. Overbeek
Geometric specification of scheduling constraints: A simplified approach to multiprocessing. Parallel Comput. 6 (3) (1988)
Ralph Butler, Terry Disz, Ewing L. Lusk, Robert Olson, Ross A. Overbeek, Rick L. Stevens
Scheduling OR-Parallelism: An Argonne Perspective. ICLP/SLP (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)
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)
Terry Disz, Ewing L. Lusk, Ross A. Overbeek
Experiments with OR-Parallel Logic Programs. ICLP (1987)
Ewing L. Lusk, William McCune, Ross A. Overbeek
ITP at Argonne National Laboratory. CADE (1986)
Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek
Parallel Logic Programming for Numeric Applications. ICLP (1986)
Barney Glickfeld, Ross A. Overbeek
A Foray Into Combinatory Logic. J. Autom. Reason. 2 (4) (1986)
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) (1986)
Ralph Butler, Ewing L. Lusk, William McCune, Ross A. Overbeek
Paths to High-Performance Automated Theorem Proving. CADE (1986)
Ewing L. Lusk, Ross A. Overbeek
Non-Horn Problems. J. Autom. Reason. 1 (1) (1985)
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) (1985)
Ewing L. Lusk, Ross A. Overbeek
Reasoning about Equality. J. Autom. Reason. 1 (2) (1985)
Bradley J. Lucier, Ross A. Overbeek
A parallel adaptive numerical scheme for hyperbolic systems for conservation laws. PPSC (1985)
Bruce D. Parrello, Ross A. Overbeek, Ewing L. Lusk
The Design of Entity-Relationship Models for General Ledger Systems. Data Knowl. Eng. 1 (2) (1985)
Ewing L. Lusk, Ross A. Overbeek
A Portable Environment for Research in Automated Reasoning. CADE (1984)
Paul K. Blackwell, Dan Kapp, Ross A. Overbeek, H. J. Spencer, Gio Wiederhold, Stanley B. Zdonik
Data Management: A Practical View (Panel). ER (1983)
G. Margrave, Ewing L. Lusk, Ross A. Overbeek
Tools for the Creation of IMS Database Designs from Entity-Relationship Diagrams. ER (1983)
Ewing L. Lusk, William McCune, Ross A. Overbeek
Logic Machine Architecture: Inference Mechanisms. CADE (1982)
Ewing L. Lusk, William McCune, Ross A. Overbeek
Logic Machine Architecture: Kernel Funtions. CADE (1982)
Ewing L. Lusk, Gene Petrie, Ross A. Overbeek
Item Tracking Entity-Relationship Models. ER (1981)
Ross A. Overbeek, Ewing L. Lusk
Data Structures and Control Architectures for Implementation of Theorem-Proving Programs. CADE (1980)
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)
Larry Wos, Ross A. Overbeek, Lawrence J. Henschen
Hyperparamodulation: A Refinement of Paramodulation. CADE (1980)
Ewing L. Lusk, Ross A. Overbeek
A DML for Entity-Relationship Models. ER (1979)
John D. McCharen, Ross A. Overbeek, Larry Wos
Problems and Experiments for and with Automated Theorem-Proving Programs. IEEE Trans. Computers 25 (8) (1976)
Ross A. Overbeek
A New Class of Automated Theorem-Proving Algorithms. J. ACM 21 (2) (1974)
Lawrence J. Henschen, Ross A. Overbeek, Larry Wos
A Theorem-Proving Language for Experimentation. Commun. ACM 17 (6) (1974)