Ebbe S. Andersen, Allan Lind-thomsen, Bjarne Knudsen, Susie E. Kristensen, Jakob H. Havgaard, Elfar Torarinsson, ...
Running title: Semi-automated RNA sequence editing
The tmRNA database (tmRDB) (2007)
Christian Zwieb, Niels Larsen, Jacek Wower
This first release of the tmRNA database (tmRDB) contains 19 tmRNA sequences, a tmRNA sequence alignment with emphasis of base pairs that are supported by comparative sequence analysis, and a...
Semiautomated improvement of RNA alignments (2007)
Andersen, Ebbe S., Lind-Thomsen, Allan, Knudsen, Bjarne, Kristensen, Susie E., Havgaard, Jakob H., Torarinsson, Elfar, ...
We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its...
The tmRDB and SRPDB resources (2006)
Andersen, Ebbe Sloth, Rosenblad, Magnus Alm, Larsen, Niels, Westergaard, Jesper Cairo, Burks, Jody, Wower, Iwona K., ...
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located...
Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis (2005)
Anderson, Iain, Sorokin, Alexei, Kapatral, Vinayak, Reznik, Gary, Bhattacharya, Anamitra, Mikhailova, Natalia, ...
Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp israelensis) were analyzed and compared with the...
The tmRDB and SRPDB resources (2005)
Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, ...
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, ...
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the...
Large nitric acid particles at the top of an Arctic stratospheric cloud (2003)
Deshler,Terry, Larsen,Niels, Weisser,Christoph, Schreiner,Jochen, Mauersberger,Konrad, Cairo,Francesco, ...
Voigt,Christiane, Larsen,Niels, Deshler,Terry, Kröger,C., Schreiner,Jochen, Mauersberger,Konrad, ...
Particle size distribution, composition, and optical properties of polar stratospheric clouds (PSCs) have been measured above northern Scandinavia during a nocturnal balloon flight within the polar...
Large nitric acid particles at the top of an Arctic stratospheric cloud (2003)
Deshler, Terry, Larsen, Niels, Weisser, Christoph, Schreiner, Jochen, Mauersberger, Konrad, Cairo, Francesco, ...
Voigt, Christiane, Larsen, Niels, Deshler, Terry, Kröger, C., Schreiner, Jochen, Mauersberger, Konrad, ...
Particle size distribution, composition, and optical properties of polar stratospheric clouds (PSCs) have been measured above northern Scandinavia during a nocturnal balloon flight within the polar...
Kapatral, Vinayak, Ivanova, Natalia, Anderson, Iain, Reznik, Gary, Bhattacharyya, Anamitra, Gardner, Warren L., ...
We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading...
The ERGOTM genome analysis and discovery system (2003)
Overbeek, Ross, Larsen, Niels, Walunas, Theresa, D'Souza, Mark, Pusch, Gordon, Selkov, Eugene, ...
The ERGOTM (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling,...
Large nitric acid containing particles above a PSC cloud (2002)
Schreiner, Jochen, Weisser, Christoph, Mauersberger, Konrad, Deshler, Terry, Larsen, Niels, Ovarlez, Joelle, ...
DOI: 10.1093/nar/gkg148 The ERGO TM genome analysis and discovery system (2002)
Ross Overbeek, Niels Larsen, Theresa Walunas, Gordon Pusch, Eugene Selkov, Konstantinos Liolios, ...
The ERGO TM
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, ...
The RDP-II (Ribosomal Database Project (2001)
Bonnie L. Maidak, Gary J. Olsen, Niels Larsen, Ross Overbeek, Michael J. Mccaughey, Carl R. Woese
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered...
Handlekompetence - mellem det individuelle og det globale / (2000)
Kandidatstudiet. Almen pædagogik.
Overbeek, Ross, Larsen, Niels, Pusch, Gordon D., DSouza, Mark, Jr, Evgeni Selkov, Kyrpides, Nikos, ...
The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/ ) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based...
The Signal Recognition Particle Database (SRPDB) (1998)
Niels Larsen, Tore Samuelsson, Christian Zwieb
This release of the SRPDB (signal recognition particle database, http://pegasus.uthct.edu/SRPDB/SRPDB. html ) adds four SRP RNA sequences (a total of 99 SRP RNA sequences), 23 SRP protein sequences...
Christian Zwieb, Niels Larsen, Jacek Wower
This first release of the tmRNA database (tmRDB) contains 19 tmRNA sequences, a tmRNA sequence alignment with emphasis of base pairs that are supported by comparative sequence analysis, and a...
The signal recognition particle database (SRPDB) (1994)
Zwieb, Christian, Larsen, Niels
The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and...
The Ribosomal Database project (1994)
Maidak, Bonnie L., Larsen, Niels, McCaughey, Michael J., Overbeek, Ross, Olsen, Gary J., Fogel, Karl, ...
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically ordered...
The signal recognition particle database (SRPDB) (1993)
Larsen, Niels, Zwieb, Christian
The SRPDB (signal recognition particle database) provides annotated SRP RNA sequences from Eucaryotes and Archaea, phylogenetically ordered and aligned with their bacterial equivalents. We also make...
The ribosomal database project (1993)
Larsen, Niels, Olsen, Gary J., Maidak, Bonnie L., McCaughey, Michael J., Overbeek, Ross, Macke, Thomas J., ...
The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal...
The Ribosomal Database Project (1992)
Olsen, Gary J., Overbeek, Ross, Larsen, Niels, Marsh, Terry L., McCaughey, Michael J., Maciukenas, Michael A., ...
The Ribosomal Database Project (RDP) compiles ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various...
SRP-RNA sequence alignment and secondary structure (1991)
Larsen, Niels, Zwieb, Christian
The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only...
DYSIK- A MODULAR SIMULATION SYSTEM FOR CONTINUOUS DYNAMIC PROCESSES (1986)
Jan E. Kofoed, Niels Larsen, Jan E. Kofoed, Niels Larsen, ...
Abstract. The report describes a revised version of a simulation system for continuous processes, DYSIM. In relation to the previous version, which was developed in 1981, the main changes are...
Hamburg, Univ., Fachbereich Medizin, Diss. 1973.
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
Overbeek, Ross, Larsen, Niels, Pusch, Gordon D., D’Souza, Mark, Jr, Evgeni Selkov, Kyrpides, Nikos, ...
The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/ ) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal...
The genome sequence of the facultative intracellular pathogen Brucella melitensis
DelVecchio, Vito G., Kapatral, Vinayak, Redkar, Rajendra J., Patra, Guy, Mujer, Cesar, Los, Tamara, ...
Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was sequenced and found...
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...
Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586
Kapatral, Vinayak, Anderson, Iain, Ivanova, Natalia, Reznik, Gary, Los, Tamara, Lykidis, Athanasios, ...
We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this anaerobe facilitates...
The ERGOTM genome analysis and discovery system
Overbeek, Ross, Larsen, Niels, Walunas, Theresa, D'Souza, Mark, Pusch, Gordon, Selkov, Eugene, ...
The ERGOTM (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling,...
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...
The Ribosomal Database Project
Olsen, Gary J., Overbeek, Ross, Larsen, Niels, Marsh, Terry L., McCaughey, Michael J., Maciukenas, Michael A., ...
The Ribosomal Database Project (RDP) compiles ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various...
Kapatral, Vinayak, Ivanova, Natalia, Anderson, Iain, Reznik, Gary, Bhattacharyya, Anamitra, Gardner, Warren L., ...
We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading...
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, ...
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the...
Andersen, Ebbe Sloth, Rosenblad, Magnus Alm, Larsen, Niels, Westergaard, Jesper Cairo, Burks, Jody, Wower, Iwona K., ...
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL with mirror sites located at Auburn University, Auburn, Alabama () and...
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
Overbeek, Ross, Larsen, Niels, Pusch, Gordon D., D’Souza, Mark, Jr, Evgeni Selkov, Kyrpides, Nikos, ...
The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/ ) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal...
The genome sequence of the facultative intracellular pathogen Brucella melitensis
DelVecchio, Vito G., Kapatral, Vinayak, Redkar, Rajendra J., Patra, Guy, Mujer, Cesar, Los, Tamara, ...
Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was sequenced and found...
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...
Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586
Kapatral, Vinayak, Anderson, Iain, Ivanova, Natalia, Reznik, Gary, Los, Tamara, Lykidis, Athanasios, ...
We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this anaerobe facilitates...
The ERGOTM genome analysis and discovery system
Overbeek, Ross, Larsen, Niels, Walunas, Theresa, D'Souza, Mark, Pusch, Gordon, Selkov, Eugene, ...
The ERGOTM (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling,...
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...
The Ribosomal Database Project
Olsen, Gary J., Overbeek, Ross, Larsen, Niels, Marsh, Terry L., McCaughey, Michael J., Maciukenas, Michael A., ...
The Ribosomal Database Project (RDP) compiles ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various...
Kapatral, Vinayak, Ivanova, Natalia, Anderson, Iain, Reznik, Gary, Bhattacharyya, Anamitra, Gardner, Warren L., ...
We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading...
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, ...
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the...
Andersen, Ebbe Sloth, Rosenblad, Magnus Alm, Larsen, Niels, Westergaard, Jesper Cairo, Burks, Jody, Wower, Iwona K., ...
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL with mirror sites located at Auburn University, Auburn, Alabama () and...
Semiautomated improvement of RNA alignments
Andersen, Ebbe S., Lind-Thomsen, Allan, Knudsen, Bjarne, Kristensen, Susie E., Havgaard, Jakob H., Torarinsson, Elfar, ...
We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its...