The ErgoTM genome analysis and discovery system

Ross Overbeek; Niels Larsen; Theresa Walunas; Mark D’ Souza; Gordon Pusch; Eugene Selkov; Konstantinos Liolios; Viktor Joukov; Denis Kaznadzey; Iain Anderson; Anamitra Bhattacharyya; Henry Burd; Warren Gardner; Paul Hanke; Vinayak Kapatral; Natalia Mikhailova; Olga Vasieva; Andrei Osterman; Veronika Vonstein; Michael Fonstein; Natalia Ivanova; Nikos Kyrpides

doi:10.1093/nar/gkg148

The Ergo^TM genome analysis and discovery system

Ross Overbeek, Niels Larsen, Theresa Walunas, Mark D’ Souza, Gordon Pusch, Eugene Selkov, Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vasieva, Andrei Osterman, Veronika Vonstein, Michael FonsteinNatalia Ivanova, Nikos Kyrpides

Medicine, General Medicine Division

Research output: Contribution to journal › Review article › peer-review

181 Scopus citations

Abstract

The ERGO™ (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes. Far beyond any conventional systems that facilitate functional assignments, ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes. The result of this multifaceted approach is to provide an extensively curated database of the largest available integration of genomes, with a vast collection of reconstructed cellular pathways spanning all domains of life. Although access to ERGO is provided only under subscription, it is already widely used by the academic community. The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.

Original language	English (US)
Pages (from-to)	164-171
Number of pages	8
Journal	Nucleic acids research
Volume	31
Issue number	1
DOIs	https://doi.org/10.1093/nar/gkg148
State	Published - Jan 1 2003

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkg148

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Overbeek, R., Larsen, N., Walunas, T., D’ Souza, M., Pusch, G., Selkov, E., 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., ... Kyrpides, N. (2003). The Ergo^TM genome analysis and discovery system. Nucleic acids research, 31(1), 164-171. https://doi.org/10.1093/nar/gkg148

Overbeek, Ross ; Larsen, Niels ; Walunas, Theresa ; D’ Souza, Mark ; Pusch, Gordon ; Selkov, Eugene ; Liolios, Konstantinos ; Joukov, Viktor ; Kaznadzey, Denis ; Anderson, Iain ; Bhattacharyya, Anamitra ; Burd, Henry ; Gardner, Warren ; Hanke, Paul ; Kapatral, Vinayak ; Mikhailova, Natalia ; Vasieva, Olga ; Osterman, Andrei ; Vonstein, Veronika ; Fonstein, Michael ; Ivanova, Natalia ; Kyrpides, Nikos. / The Ergo^TM genome analysis and discovery system. In: Nucleic acids research. 2003 ; Vol. 31, No. 1. pp. 164-171.

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title = "The ErgoTM genome analysis and discovery system",

abstract = "The ERGO{\texttrademark} (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes. Far beyond any conventional systems that facilitate functional assignments, ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes. The result of this multifaceted approach is to provide an extensively curated database of the largest available integration of genomes, with a vast collection of reconstructed cellular pathways spanning all domains of life. Although access to ERGO is provided only under subscription, it is already widely used by the academic community. The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.",

author = "Ross Overbeek and Niels Larsen and Theresa Walunas and {D{\textquoteright} Souza}, Mark and Gordon Pusch and Eugene Selkov and Konstantinos Liolios and Viktor Joukov and Denis Kaznadzey and Iain Anderson and Anamitra Bhattacharyya and Henry Burd and Warren Gardner and Paul Hanke and Vinayak Kapatral and Natalia Mikhailova and Olga Vasieva and Andrei Osterman and Veronika Vonstein and Michael Fonstein and Natalia Ivanova and Nikos Kyrpides",

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doi = "10.1093/nar/gkg148",

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Overbeek, R, Larsen, N, Walunas, T, D’ Souza, M, Pusch, G, Selkov, E, 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 2003, 'The Ergo^TM genome analysis and discovery system', Nucleic acids research, vol. 31, no. 1, pp. 164-171. https://doi.org/10.1093/nar/gkg148

The Ergo^TM genome analysis and discovery system. / Overbeek, Ross; Larsen, Niels; Walunas, Theresa; D’ Souza, Mark; Pusch, Gordon; Selkov, Eugene; Liolios, Konstantinos; Joukov, Viktor; Kaznadzey, Denis; Anderson, Iain; Bhattacharyya, Anamitra; Burd, Henry; Gardner, Warren; Hanke, Paul; Kapatral, Vinayak; Mikhailova, Natalia; Vasieva, Olga; Osterman, Andrei; Vonstein, Veronika; Fonstein, Michael; Ivanova, Natalia; Kyrpides, Nikos.

In: Nucleic acids research, Vol. 31, No. 1, 01.01.2003, p. 164-171.

Research output: Contribution to journal › Review article › peer-review

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T1 - The ErgoTM genome analysis and discovery system

AU - Overbeek, Ross

AU - Larsen, Niels

AU - Walunas, Theresa

AU - D’ Souza, Mark

AU - Pusch, Gordon

AU - Selkov, Eugene

AU - Liolios, Konstantinos

AU - Joukov, Viktor

AU - Kaznadzey, Denis

AU - Anderson, Iain

AU - Bhattacharyya, Anamitra

AU - Burd, Henry

AU - Gardner, Warren

AU - Hanke, Paul

AU - Kapatral, Vinayak

AU - Mikhailova, Natalia

AU - Vasieva, Olga

AU - Osterman, Andrei

AU - Vonstein, Veronika

AU - Fonstein, Michael

AU - Ivanova, Natalia

AU - Kyrpides, Nikos

PY - 2003/1/1

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N2 - The ERGO™ (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes. Far beyond any conventional systems that facilitate functional assignments, ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes. The result of this multifaceted approach is to provide an extensively curated database of the largest available integration of genomes, with a vast collection of reconstructed cellular pathways spanning all domains of life. Although access to ERGO is provided only under subscription, it is already widely used by the academic community. The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.

AB - The ERGO™ (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes. Far beyond any conventional systems that facilitate functional assignments, ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes. The result of this multifaceted approach is to provide an extensively curated database of the largest available integration of genomes, with a vast collection of reconstructed cellular pathways spanning all domains of life. Although access to ERGO is provided only under subscription, it is already widely used by the academic community. The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.

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