Microbial co-habitation and lateral gene transfer: what transposases can tell us (2009)
Hooper, Sean D, Mavromatis, Konstantinos, Kyrpides, Nikos C
Abstract Background Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change...
Hooper, Sean D., Anderson, Iain J., Pati, Amrita, Dalevi, Daniel, Mavromatis, Konstantinos, Kyrpides, Nikos C.
In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes...
IMG ER: a system for microbial genome annotation expert review and curation (2009)
Markowitz, Victor M., Mavromatis, Konstantinos, Ivanova, Natalia N., Chen, I-Min A., Chu, Ken, Kyrpides, Nikos C.
Motivation: A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the...
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans (2008)
Podar, Mircea, Anderson, Iain, Makarova, Kira S, Elkins, James G, Ivanova, Natalia, Wall, Mark A, ...
Abstract Background The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea....
Bland, Charles, Ramsey, Teresa L., Sabree, Fareedah, Lowe, Micheal, Brown, Kyndall, Kyrpides, Nikos C., ...
IMG/M: A data management and analysis system for metagenomes (2008)
Markowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, ...
Markowitz, Victor M., Szeto, Ernest, Palaniappan, Krishna, Grechkin, Yuri, Chu, Ken, Chen, I-Min A., ...
Metagenomic analysis of phosphorus removing sludge communities (2008)
Garcia Martin, Hector, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie, McHardy, Alice C., ...
Enhanced Biological Phosphorus Removal (EBPR) is not well understood at the metabolic level despite being one of the best-studied microbially-mediated industrial processes due to its ecological and...
Using IMG: Comparative Analysis with the Integrated Microbial Genomes System (2008)
Markowitz, Victor M., Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Szeto, Ernest, ...
Victor M. Markowitz, Natalia Ivanova, Ernest Szeto, Frank Korzeniewski, Athanasios Lykidis, Iain Anderson, ...
An experimental metagenome data management and analysis system Vol. 22 no. 14 2006, pages e359–e367 doi:10.1093/bioinformatics/btl217
Liolios, Konstantinos, Mavromatis, Konstantinos, Tavernarakis, Nektarios, Kyrpides, Nikos C.
The Genomes On Line Database (GOLD) is a comprehensive resource that provides information on genome and metagenome projects worldwide. Complete and ongoing projects and their associated metadata can...
Markowitz, Victor M., Szeto, Ernest, Palaniappan, Krishna, Grechkin, Yuri, Chu, Ken, Chen, I-Min A., ...
The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes...
IMG/M: a data management and analysis system for metagenomes (2008)
Markowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, ...
IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data...
Bland, Charles, Ramsey, Teresa L, Sabree, Fareedah, Lowe, Micheal, Brown, Kyndall, Kyrpides, Nikos C, ...
Abstract Background Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract...
Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis, Nikos C. Kyrpides
status of genomic and metagenomic projects and their associated metadata
Nucleic Acids Research, 2007, 1–5 (2007)
Victor M. Markowitz, Natalia N. Ivanova, Ernest Szeto, Ken Chu, Daniel Dalevi, ...
IMG/M: a data management and analysis system for metagenomes
Use of simulated data sets to evaluate the fidelity of Metagenomic processing methods (2006)
Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerri, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., ...
Symbiosis insights through metagenomic analysis of a microbial consortium (2006)
Woyke, Tanja, Teeling, Hanno, Ivanova, Natalia N., Hunteman, Marcel, Richter, Michael, Gloeckner, Frank Oliver, ...
An Experimental Metagenome Data Management and Analysis System (2006)
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Ivanova, Natalia N., Kyrpides, Nikos C., ...
Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System (2006)
Kyrpides, Nikos C., Markowitz, Victor M.
Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system...
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide (2006)
Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos C. Kyrpides
genome projects worldwide
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities (2006)
Martín, Hector Garcia, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W., McHardy, Alice C., ...
Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well...
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide (2006)
Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Kyrpides, Nikos C.
The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates...
The integrated microbial genomes (IMG) system (2006)
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, ...
The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete...
An experimental metagenome data management and analysis system (2006)
Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, ...
The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis,...
Feil, Helene, Feil, William S., Chain, Patrick, Larimer, Frank, DiBartolo, Genevieve, Copeland, Alex, ...
The complete genomic sequence of Pseudomonas syringae pathovar syringae B728a (Pss B728a), has been determined and is compared with that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). These...
The Integrated Microbial Genomes (IMG) System: A Case Study (2005)
Victor M. Markowitz, Frank Korzeniewski, Ernest Szeto, Natalia Ivanova, Nikos C. Kyrpides
Biological data management includes the traditional areas of data generation, acquisition, modelling, integration, and analysis. Although numerous academic biological data management systems are...
doi:10.1093/nar/gkj024 The integrated microbial genomes (IMG) system (2005)
Victor M. Markowitz, Frank Korzeniewski, Ernest Szeto, Greg Werner, Anu Padki, Xueling Zhao, ...
The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete...
Bhattacharyya, Anamitra, Stilwagen, Stephanie, Reznik, Gary, Feil, Helene, Feil, William S., Anderson, Iain, ...
Bhattacharyya, Anamitra, Stilwagen, Stephanie, Reznik, Gary, Feil, Helene, Feil, William S., Anderson, Iain, ...
Kyrpides, Nikos C., Ouzounis, Christos A., Iliopoulos, Ioannis, Vonstein, Veronika, Overbeek, Ross
The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif...
Kyrpides, Nikos C., Ouzounis, Christos A.
Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal...
Universally conserved translation initiation factors
Kyrpides, Nikos C., Woese, Carl R.
The process by which translation is initiated has long been considered similar in Bacteria and Eukarya but accomplished by a different unrelated set of factors in the two cases. This not only implies...
Kyrpides, Nikos C., Woese, Carl R.
As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of...
Kyrpides, Nikos C., Ouzounis, Christos A., Iliopoulos, Ioannis, Vonstein, Veronika, Overbeek, Ross
The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif...
Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains
Bhattacharyya, Anamitra, Stilwagen, Stephanie, Ivanova, Natalia, D'Souza, Mark, Bernal, Axel, Lykidis, Athanasios, ...
Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative...
Bhattacharyya, Anamitra, Stilwagen, Stephanie, Reznik, Gary, Feil, Helene, Feil, William S., Anderson, Iain, ...
Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences...
Feil, Helene, Feil, William S., Chain, Patrick, Larimer, Frank, DiBartolo, Genevieve, Copeland, Alex, ...
The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been determined and is compared with that of P. syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of...
The integrated microbial genomes (IMG) system
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, ...
The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete...
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Kyrpides, Nikos C.
The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates...
Kyrpides, Nikos C., Ouzounis, Christos A.
Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal...
Universally conserved translation initiation factors
Kyrpides, Nikos C., Woese, Carl R.
The process by which translation is initiated has long been considered similar in Bacteria and Eukarya but accomplished by a different unrelated set of factors in the two cases. This not only implies...
Kyrpides, Nikos C., Woese, Carl R.
As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of...
Kyrpides, Nikos C., Ouzounis, Christos A., Iliopoulos, Ioannis, Vonstein, Veronika, Overbeek, Ross
The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif...
Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains
Bhattacharyya, Anamitra, Stilwagen, Stephanie, Ivanova, Natalia, D'Souza, Mark, Bernal, Axel, Lykidis, Athanasios, ...
Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative...
Bhattacharyya, Anamitra, Stilwagen, Stephanie, Reznik, Gary, Feil, Helene, Feil, William S., Anderson, Iain, ...
Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences...
Feil, Helene, Feil, William S., Chain, Patrick, Larimer, Frank, DiBartolo, Genevieve, Copeland, Alex, ...
The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been determined and is compared with that of P. syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of...
The integrated microbial genomes (IMG) system
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, ...
The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete...
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Kyrpides, Nikos C.
The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates...
Bland, Charles, Ramsey, Teresa L, Sabree, Fareedah, Lowe, Micheal, Brown, Kyndall, Kyrpides, Nikos C, ...
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
Markowitz, Victor M., Szeto, Ernest, Palaniappan, Krishna, Grechkin, Yuri, Chu, Ken, Chen, I-Min A., ...
The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes...
IMG/M: a data management and analysis system for metagenomes
Markowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, ...
IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data...
Liolios, Konstantinos, Mavromatis, Konstantinos, Tavernarakis, Nektarios, Kyrpides, Nikos C.
The Genomes On Line Database (GOLD) is a comprehensive resource that provides information on genome and metagenome projects worldwide. Complete and ongoing projects and their associated metadata can...
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
Podar, Mircea, Anderson, Iain, Makarova, Kira S, Elkins, James G, Ivanova, Natalia, Wall, Mark A, ...
Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans.
Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii
Mavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Hooper, Sean D., Sun, Hui, ...
Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The...
Hooper, Sean D., Anderson, Iain J., Pati, Amrita, Dalevi, Daniel, Mavromatis, Konstantinos, Kyrpides, Nikos C.
In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes...
Microbial co-habitation and lateral gene transfer: what transposases can tell us
Hooper, Sean D, Mavromatis, Konstantinos, Kyrpides, Nikos C
Interactions between microbial communities are revealed using a network of lateral gene transfer events.