GOBASE: an organelle genome database (2009)
OBrien, Emmet A., Zhang, Yue, Wang, Eric, Marie, Veronique, Badejoko, Wole, Lang, B. Franz, ...
The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (∼913 000) and chloroplast-encoded sequences (∼250 000) from a...
Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases (2009)
Shen, Yao-Qing, Lang, B. Franz, Burger, Gertraud
Acyl-CoA dehydrogenases (ACADs), which are key enzymes in fatty acid and amino acid catabolism, form a large, pan-taxonomic protein family with at least 13 distinct subfamilies. Yet most reported...
Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2 (2008)
Kannan, Sivakumar, Burger, Gertraud
Abstract Background In a previous study, we conducted a large-scale similarity-free function prediction of mitochondrion-encoded hypothetical proteins, by which the hypothetical gene murf1...
Tadepally, Hamsa D, Burger, Gertraud, Aubry, Muriel
Abstract Background C2H2 zinc finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and one of the largest gene families in mammals. Often arranged in clusters in...
Iñaki Ruiz-trillo, Andrew J. Roger, Gertraud Burger, Michael W. Gray, Franz Lang
Non standard abbreviations ML: maximum likelihood EST: expressed sequence taq MAGI: membrane-associated guanylate kinase ANTP: Antennapedia PRD: paired
Methodology for Constructing Problem Definitions in Bioinformatics (2008)
Motivation: A recurrent criticism is that certain bioinformatics tools do not account for crucial biology and therefore fail answering the targeted biological question. We posit that the single most...
A Phylogenomic Investigation into the Origin of Metazoa (2008)
Ruiz-Trillo, Iñaki, Roger, Andrew J., Burger, Gertraud, Gray, Michael W., Lang, B. Franz
The evolution of multicellular animals (Metazoa) from their unicellular ancestors was a key transition that was accompanied by the emergence and diversification of gene families associated with...
Abstract Background Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for...
Bmc Bioinformatics, Yao Qing Shen, Gertraud Burger
'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs) (2007)
O'Brien, Emmet A., Koski, Liisa B., Zhang, Yue, Yang, LiuSong, Wang, Eric, Gray, Michael W., ...
The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and...
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs) (2006)
Emmet A. O’brien, Liisa B. Koski, Yue Zhang, Liusong Yang, Eric Wang, Michael W. Gray, ...
The TBestDB database contains 370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and...
GOBASE—a database of organelle and bacterial genome information (2006)
Emmet A. O’brien, Yue Zhang, Liusong Yang, Eric Wang, Veronique Marie, B. Franz Lang, ...
The organelle genome database GOBASE is now in its twelfth release, and includes 350 000 mitochondrial sequences and 118 000 chloroplast sequences, roughly a 3-fold expansion since previously...
GOBASE--a database of organelle and bacterial genome information (2006)
O'Brien, Emmet A., Zhang, Yue, Yang, LiuSong, Wang, Eric, Marie, Veronique, Lang, B. Franz, ...
The organelle genome database GOBASE is now in its twelfth release, and includes 350 000 mitochondrial sequences and 118 000 chloroplast sequences, roughly a 3-fold expansion since previously...
AutoFACT: An Automatic Functional Annotation and Classification Tool (2005)
Koski, Liisa B, Gray, Michael W, Lang, B Franz, Burger, Gertraud
Abstract Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or...
AutoFACT: An Automatic Functional Annotation and Classification Tool (2005)
Koski, Liisa, Gray, Michael, Lang, B. Franz, Burger, Gertraud
Affiliation: Centre Robert-Cedergren de l'Université de Montréal en bio-informatique et génomique & Département de biochimie, Université de Montréal
Hauth, Amy M., Maier, Uwe G., Lang, B. Franz, Burger, Gertraud
To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas...
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis (2003)
Badidi, Elarbi, De Sousa, Cristina, Lang, B, Burger, Gertraud
Abstract Background Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools. Due to the heterogeneity...
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis (2003)
Badidi, Elarbi, De Sousa, Cristina, Lang, Franz Bernd, Burger, Gertraud
Affiliation: Département de biochimie, Faculté de médecine, Université de Montréal
GOBASE – a database of mitochondrial and chloroplast information (2003)
Emmet A. O’brien, Elarbi Badidi, Ania Barbasiewicz, Cristina Desousa, B. Franz Lang, Gertraud Burger
GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130...
Bmc Bioinformatics, Elarbi Badidi, Cristina De Sousa, B Franz Lang, Gertraud Burger, Gertraud Burger
AnaBench: a Web/CORBA-based workbench for biomolecular
The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b (2003)
Burger, Gertraud, Lang, B. Franz, Braun, Hans-Peter, Marx, Stefanie
ymf39 is a conserved hypothetical protein‐coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39...
GOBASE--a database of mitochondrial and chloroplast information (2003)
O'Brien, Emmet A., Badidi, Elarbi, Barbasiewicz, Ania, DeSousa, Cristina, Lang, B. Franz, Burger, Gertraud
GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over...
Marx, Stefanie, Baumgärtner, Maja, Kunnan, Sivakumar, Braun, Hans-Peter, Lang, B. Franz, Burger, Gertraud
In eubacteria, the respiratory bc1 complex (complex III) consists of three or four different subunits, whereas that of mitochondria, which have descended from an α-proteobacterial endosymbiont,...
The origin and early evolution of mitochondria (2001)
Gray, Michael W, Burger, Gertraud, Lang, B Franz
Abstract Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial...
GOBASE: the organelle genome database (2001)
Shimko, Nelli, Liu, Lin, Lang, B. Franz, Burger, Gertraud
GOBASE (http://megasun.bch.umontreal.ca/gobase/) is a network-accessible biological database, which is unique in bringing together diverse biological data on organelles with...
Chesnick, Joby M., Goff, Megan, Graham, James, Ocampo, Christopher, Lang, B. Franz, Seif, Elias, ...
This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping...
Genome structure and gene content in protist mitochondrial DNAs (1998)
Michael W. Gray, B. Franz Lang, Robert Cedergren, G. Brian Golding, Claude Lemieux, David Sankoff, ...
Although the collection of completely sequenced mitochondrial genomes is expanding rapidly, only recently has a phylogenetically broad representation of mtDNA sequences from protists (mostly...
The Organelle Genome Database Project (GOBASE (1998)
Maria Korab-laskowska, Pierre Rioux, Nicolas Brossard, Timothy G. Littlejohn, Michael W. Gray, B. Franz Lang, ...
The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the...
The Organelle Genome Database Project (GOBASE) (1998)
Maria Korab-Laskowska, Pierre Rioux, Nicolas Brossard, Timothy G. Littlejohn, Michael W. Gray, B. Franz Lang, ...
The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the...
Wolf, Gabriele, Burger, Gertraud, Lang, B.Franz, Kück, Ulrich
The mitochondrial DNA from the colourless alga Prototheca wickerhamit contains two mosaic genes as was revealed from complete sequencing of the circular extranuclear genome. The genes for the large...
Lang, B. Franz, Burger, Gertraud
We have developed a collection of programs for manipulation and analysis of nucleotide and protein sequences. The package was written in Fortran 77 on a Siriusi/Victor microcomputer which can be...
GOBASE: the organelle genome database
Shimko, Nelli, Liu, Lin, Lang, B. Franz, Burger, Gertraud
GOBASE (http://megasun.bch.umontreal.ca/gobase/) is a network-accessible biological database, which is unique in bringing together diverse biological data on organelles with taxonomically broad...
Chesnick, Joby M., Goff, Megan, Graham, James, Ocampo, Christopher, Lang, B. Franz, Seif, Elias, ...
This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping...
The origin and early evolution of mitochondria
Gray, Michael W, Burger, Gertraud, Lang, B Franz
Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial...
The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b
Burger, Gertraud, Lang, B. Franz, Braun, Hans-Peter, Marx, Stefanie
ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39 from...
GOBASE—a database of mitochondrial and chloroplast information
O'Brien, Emmet A., Badidi, Elarbi, Barbasiewicz, Ania, DeSousa, Cristina, Lang, B. Franz, Burger, Gertraud
GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130...
Unique mitochondrial genome architecture in unicellular relatives of animals
Burger, Gertraud, Forget, Lise, Zhu, Yun, Gray, Michael W., Lang, B. Franz
Animal mtDNAs are typically small (≈16 kbp), circular-mapping molecules that encode 37 or fewer tightly packed genes. Here we investigate whether similarly compact mitochondrial genomes are also...
Nedelcu, Aurora M., Lee, Robert W., Lemieux, Claude, Gray, Michael W., Burger, Gertraud
Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced–derived, Chlamydomonas-like type and an ancestral, Prototheca-like type....
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
Badidi, Elarbi, De Sousa, Cristina, Lang, B Franz, Burger, Gertraud
Unique Mitochondrial Genome Structure in Diplonemids, the Sister Group of Kinetoplastids
Marande, William, Lukeš, Julius, Burger, Gertraud
Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules:...
AutoFACT: An Automatic Functional Annotation and Classification Tool
Koski, Liisa B, Gray, Michael W, Lang, B Franz, Burger, Gertraud
Hauth, Amy M., Maier, Uwe G., Lang, B. Franz, Burger, Gertraud
To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas...
GOBASE—a database of organelle and bacterial genome information
O'Brien, Emmet A., Zhang, Yue, Yang, LiuSong, Wang, Eric, Marie, Veronique, Lang, B. Franz, ...
The organelle genome database GOBASE is now in its twelfth release, and includes 350 000 mitochondrial sequences and 118 000 chloroplast sequences, roughly a 3-fold expansion since previously...
Breton, Sophie, Burger, Gertraud, Stewart, Donald T., Blier, Pierre U.
Marine mussels of the genus Mytilus have an unusual mode of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Female mussels are homoplasmic for the F mitotype,...
GOBASE: the organelle genome database
Shimko, Nelli, Liu, Lin, Lang, B. Franz, Burger, Gertraud
GOBASE (http://megasun.bch.umontreal.ca/gobase/) is a network-accessible biological database, which is unique in bringing together diverse biological data on organelles with taxonomically broad...
Chesnick, Joby M., Goff, Megan, Graham, James, Ocampo, Christopher, Lang, B. Franz, Seif, Elias, ...
This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping...
The origin and early evolution of mitochondria
Gray, Michael W, Burger, Gertraud, Lang, B Franz
Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial...
The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b
Burger, Gertraud, Lang, B. Franz, Braun, Hans-Peter, Marx, Stefanie
ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39 from...
GOBASE—a database of mitochondrial and chloroplast information
O'Brien, Emmet A., Badidi, Elarbi, Barbasiewicz, Ania, DeSousa, Cristina, Lang, B. Franz, Burger, Gertraud
GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130...
Unique mitochondrial genome architecture in unicellular relatives of animals
Burger, Gertraud, Forget, Lise, Zhu, Yun, Gray, Michael W., Lang, B. Franz
Animal mtDNAs are typically small (≈16 kbp), circular-mapping molecules that encode 37 or fewer tightly packed genes. Here we investigate whether similarly compact mitochondrial genomes are also...
Nedelcu, Aurora M., Lee, Robert W., Lemieux, Claude, Gray, Michael W., Burger, Gertraud
Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced–derived, Chlamydomonas-like type and an ancestral, Prototheca-like type....
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
Badidi, Elarbi, De Sousa, Cristina, Lang, B Franz, Burger, Gertraud
Unique Mitochondrial Genome Structure in Diplonemids, the Sister Group of Kinetoplastids
Marande, William, Lukeš, Julius, Burger, Gertraud
Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules:...
AutoFACT: An Automatic Functional Annotation and Classification Tool
Koski, Liisa B, Gray, Michael W, Lang, B Franz, Burger, Gertraud
Hauth, Amy M., Maier, Uwe G., Lang, B. Franz, Burger, Gertraud
To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas...
GOBASE—a database of organelle and bacterial genome information
O'Brien, Emmet A., Zhang, Yue, Yang, LiuSong, Wang, Eric, Marie, Veronique, Lang, B. Franz, ...
The organelle genome database GOBASE is now in its twelfth release, and includes 350 000 mitochondrial sequences and 118 000 chloroplast sequences, roughly a 3-fold expansion since previously...
Breton, Sophie, Burger, Gertraud, Stewart, Donald T., Blier, Pierre U.
Marine mussels of the genus Mytilus have an unusual mode of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Female mussels are homoplasmic for the F mitotype,...
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
O'Brien, Emmet A., Koski, Liisa B., Zhang, Yue, Yang, LiuSong, Wang, Eric, Gray, Michael W., ...
The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and...
Gile, Gillian H., Faktorová, Drahomíra, Castlejohn, Christina A., Burger, Gertraud, Lang, B. Franz, Farmer, Mark A., ...
GOBASE: an organelle genome database
O’Brien, Emmet A., Zhang, Yue, Wang, Eric, Marie, Veronique, Badejoko, Wole, Lang, B. Franz, ...
The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (∼913 000) and chloroplast-encoded sequences (∼250 000) from a...
Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication
Ma, Li-Jun, Ibrahim, Ashraf S., Skory, Christopher, Grabherr, Manfred G., Burger, Gertraud, Butler, Margi, ...
Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a...
Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases
Shen, Yao-Qing, Lang, B. Franz, Burger, Gertraud
Acyl-CoA dehydrogenases (ACADs), which are key enzymes in fatty acid and amino acid catabolism, form a large, pan-taxonomic protein family with at least 13 distinct subfamilies. Yet most reported...