Gaudet, Pascale, Chisholm, Rex, Berardini, Tanya, Dimmer, Emily, Engel, Stacia R., Fey, Petra, ...
The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly...
FlyBase: enhancing Drosophila Gene Ontology annotations (2009)
Tweedie, Susan, Ashburner, Michael, Falls, Kathleen, Leyland, Paul, McQuilton, Peter, Marygold, Steven, ...
FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular...
Michael Ashburner, Nathan Goodman
Databases for biologists are becoming increasingly important. Some of these can be regarded as ‘core ’ resources, such as the bibliographic databases, whereas others are of greater interest to...
Luís Teixeira, Álvaro Ferreira, Michael Ashburner
Wolbachia are vertically transmitted, obligatory intracellular bacteria that infect a great number of species of arthropods and nematodes. In insects, they are mainly known for disrupting the...
Taylor, Chris, Field, Dawn, Sansone, Susanna-Assunta, Apweiler, Rolf, Ashburner, Michael, Ball, Cathy, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those...
Calling on a million minds for community annotation in WikiProteins (2008)
Mons, Barend, Ashburner, Michael, Chichester, Christine, Van Mulligen, Erik, Weeber, Marc, Den Dunnen, Johan, ...
Abstract WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data...
NLP and Phenotypes: using Ontologies to link Human Diseases to Animal Models (2008)
Washington, N., Gibson, M., Mungall, C.J., Ashburner, Michael, Gkoutos, G., Westerfield, M., ...
The path to disease gene discovery in humans is often a lengthy one, but can be significantly shortened if links between human and model organism phenotypes are readily available. Collecting and...
Ashburner, Michael, Leser, Ulf, Rebholz-Schuhmann, Dietrich
Researchers in Text Mining and researchers active in developing ontological resources provide solutions to preserve semantic information properly, i.e. in ontologies and/or fact databases....
ChEBI: a database and ontology for chemical entities of biological interest (2008)
Degtyarenko, Kirill, De Matos, Paula, Ennis, Marcus, Hastings, Janna, Zbinden, Martin, McNaught, Alan, ...
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either...
The ribosomal protein genes and Minuteloci of Drosophila melanogaster (2007)
Marygold, Steven J, Roote, John, Reuter, Gunter, Lambertsson, Andrew, Ashburner, Michael, Millburn, Gillian H, ...
Abstract Background Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster...
FlyMine: an integrated database for Drosophilaand Anophelesgenomics (2007)
Lyne, Rachel, Smith, Richard, Rutherford, Kim, Wakeling, Matthew, Varley, Andrew, Guillier, Francois, ...
Abstract FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main...
Principles of Genome Evolution in the Drosophila melanogaster Species Group (2007)
José M. Ranz, Damien Maurin, Yuk S. Chan, Marcin Von Grotthuss, LaDeana W. Hillier, John Roote, ...
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although...
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration (2007)
Smith, Barry, Ashburner, Michael, Rosse, Cornelius, Bard, Jonathan, Bug, William, Ceusters, Werner, ...
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of...
Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, ...
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of...
Rubin, Daniel L., Lewis, Suzanna E., Mungall, Chris J., Misra, Sima, Westerfield, Monte, Ashburner, Michael, ...
The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to...
Bergman, Casey M, Quesneville, Hadi, Anxolabéhère, Dominique, Ashburner, Michael
The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the...
Bergman, Casey M, Quesneville, Hadi, Anxolabéhère, Dominique, Ashburner, Michael
The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the...
Combined Evidence Annotation of Transposable Elements in Genome Sequences (2005)
Hadi Quesneville, Casey M. Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, ...
Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most...
Combined evidence annotation of transposable elements in genome sequences (2005)
Quesneville, Hadi, Bergman, Casey, Andrieu, Olivier, Autard, Delphine, Nouaud, Danielle, Ashburner, Michael, ...
Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most...
Combined evidence annotation of transposable elements in genome sequences (2005)
Quesneville, Hadi, Bergman, Casey, Andrieu, Olivier, Autard, Delphine, Nouaud, Danielle, Ashburner, Michael, ...
Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most...
Drosophila melanogaster: A case study of a model genomic sequence and its consequences (2005)
Ashburner, Michael, Bergman, Casey M.
The sequencing and annotation of the Drosophila melanogaster genome, first published in 2000 through collaboration between Celera Genomics and the Drosophila Genome Projects, has provided a number of...
A short study on the success of the gene ontology (2004)
Michael Bada, Robert Stevens, Carole Goble, A Gil, Michael Ashburner, Judith A. Blake, ...
While most ontologies have been used only by the groups who created them and for their initially defined purposes, the Gene Ontology (GO), an evolving structured controlled vocabulary of nearly...
A short study on the success of the gene ontology (2004)
Michael Bada, Robert Stevens, Carole Goble, A Gil, Michael Ashburner, Judith A. Blake, ...
While most ontologies have been used only by the groups who created them and for their initially defined purposes, the Gene Ontology (GO), an evolving structured controlled vocabulary of nearly...
Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster (2003)
Mi, Huaiyu, Vandergriff, Jody, Campbell, Michael, Narechania, Apurva, Majoros, William, Lewis, Suzanna, ...
The functional classification of genes on a genome-wide scale is now in its infancy, and we make a first attempt to assess existing methods and identify sources of error. To this end, we compared two...
Mapping and identification of essential gene functions on the X chromosome of Drosophila (2002)
Peter, Annette, Schoettler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective (2002)
Joshua S Kaminker, Brent Kronmiller, Robert Svirskas, Eep Patel, Erwin Frise, David A, ...
Background: Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
Betrán, Esther, Ashburner, Michael
It has recently been discovered that the Alcohol dehydrogenase and Alcohol dehydrogenase–related genes of Drosophila melanogaster and closely related species constitute a single transcription unit...
Saunders, Robert D.C., Glover, David M., Ashburner, Michael, Siden-Kiamos, Inga, Louis, Christos, Monastirioti, Maria, ...
A novel alternative to microcloning for the production of region specific chromosomal DNA is described. In this method, ‘microamplification’, single bands are dissected from polytene chromosomes...
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Misra, Sima, Crosby, Madeline A, Mungall, Christopher J, Matthews, Beverley B, Campbell, Kathryn S, Hradecky, Pavel, ...
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to...
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective
Kaminker, Joshua S, Bergman, Casey M, Kronmiller, Brent, Carlson, Joseph, Svirskas, Robert, Patel, Sandeep, ...
Using Release 3 of the euchromatic genomic sequence of Drosophila melanogaster, 85 known and eight novel families of transposable element have been identified, varying in copy number from one to 146....
Systematic determination of patterns of gene expression during Drosophila embryogenesis
Tomancak, Pavel, Beaton, Amy, Weiszmann, Richard, Kwan, Elaine, Shu, ShengQiang, Lewis, Suzanna E, ...
As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of...
A hat trick - Plasmodium, Anopheles and Homo
The genomes of the malaria parasite, its vector and its host are now sequenced. But will it offer hope to the millions who die from malaria each year?
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster
Mi, Huaiyu, Vandergriff, Jody, Campbell, Michael, Narechania, Apurva, Majoros, William, Lewis, Suzanna, ...
The functional classification of genes on a genome-wide scale is now in its infancy, and we make a first attempt to assess existing methods and identify sources of error. To this end, we compared two...
Molecular characterization of the singed wings locus of Drosophila melanogaster
Schwartz, Yuri B, Boykova, Tatiana, Belyaeva, Elena S, Ashburner, Michael, Zhimulev, Igor F
Bard, Jonathan, Rhee, Seung Y, Ashburner, Michael
An ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds is described. It includes over 680 cell types. These cell types are classified under several generic categories...
Mapping and identification of essential gene functions on the X chromosome of Drosophila
Peter, Annette, Schöttler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
The Sequence Ontology: a tool for the unification of genome annotations
Eilbeck, Karen, Lewis, Suzanna E, Mungall, Christopher J, Yandell, Mark, Stein, Lincoln, Durbin, Richard, ...
The goal of the Sequence Ontology (SO) project is to produce a structured controlled vocabulary with a common set of terms and definitions for parts of a genomic annotation, and to describe the...
Combined Evidence Annotation of Transposable Elements in Genome Sequences
Quesneville, Hadi, Bergman, Casey M, Andrieu, Olivier, Autard, Delphine, Nouaud, Danielle, Ashburner, Michael, ...
Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most...
A lethal locus (l(2)br7;35B6-10), near Adh on chromosome arm 2L of D. melanogaster, is identified with Plunkett's dominant suppressor of Hairless (H). Of eight new alleles, seven act as dominant...
Genetic Characterization of the 87c Region of the Third Chromosome of DROSOPHILA MELANOGASTER
Gausz, Janos, Bencze, Gabor, Gyurkovics, Henrik, Ashburner, Michael, Ish-Horowicz, David, Holden, Jeanette J.
Ethyl methanesulphonate (EMS) was used to induce 39 lethal and 13 karmoisin mutations within Df(3R)kar3J, a nine-band deficiency extending from 87C1 to 87C9 (inclusive). Five complementation groups...
Kiehart, Daniel P., Franke, Josef D., Chee, Mark K., Montague, R. A., Chen, Tung-ling, Roote, John, ...
Myosin VIIs provide motor function for a wide range of eukaryotic processes. We demonstrate that mutations in crinkled (ck) disrupt the Drosophila myosin VIIA heavy chain. The ck/myoVIIA protein is...
Barbash, Daniel A, Ashburner, Michael
Hybrid daughters of crosses between Drosophila melanogaster females and males from the D. simulans species clade are fully viable at low temperature but have agametic ovaries and are thus sterile. We...
Ryder, Edward, Blows, Fiona, Ashburner, Michael, Bautista-Llacer, Rosa, Coulson, Darin, Drummond, Jenny, ...
We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P...
Getting a buzz out of the bee genome
Ashburner, Michael, Kyriacou, Charalambos P
The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further...
Bergman, Casey M, Quesneville, Hadi, Anxolabéhère, Dominique, Ashburner, Michael
An analysis of high-resolution transposable element annotations in Drosophila melanogaster suggests the existence of a global surveillance system against the majority of transposable elements...
EGASP: the human ENCODE Genome Annotation Assessment Project
Guigó, Roderic, Flicek, Paul, Abril, Josep F, Reymond, Alexandre, Lagarde, Julien, Denoeud, France, ...
Principles of Genome Evolution in the Drosophila melanogaster Species Group
Ranz, José M, Maurin, Damien, Chan, Yuk S, Von Grotthuss, Marcin, Hillier, LaDeana W, Roote, John, ...
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although...
The DrosDel Deletion Collection: A Drosophila Genomewide Chromosomal Deficiency Resource
Ryder, Edward, Ashburner, Michael, Bautista-Llacer, Rosa, Drummond, Jenny, Webster, Jane, Johnson, Glynnis, ...
We describe a second-generation deficiency kit for Drosophila melanogaster composed of molecularly mapped deletions on an isogenic background, covering ∼77% of the Release 5.1 genome. Using a...
ChEBI: a database and ontology for chemical entities of biological interest
Degtyarenko, Kirill, De Matos, Paula, Ennis, Marcus, Hastings, Janna, Zbinden, Martin, McNaught, Alan, ...
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either...
The ribosomal protein genes and Minute loci of Drosophila melanogaster
Marygold, Steven J, Roote, John, Reuter, Gunter, Lambertsson, Andrew, Ashburner, Michael, Millburn, Gillian H, ...
A combined bioinformatic and genetic approach was used to conduct a systematic analysis of the relationship between ribosomal protein genes and Minute loci in Drosophila melanogaster, allowing the...
FlyMine: an integrated database for Drosophila and Anopheles genomics
Lyne, Rachel, Smith, Richard, Rutherford, Kim, Wakeling, Matthew, Varley, Andrew, Guillier, Francois, ...
This novel web-based database provides unique accessibility and querying of integrated genomic and proteomic data for Drosophila and Anopheles.
Calling on a million minds for community annotation in WikiProteins
Mons, Barend, Ashburner, Michael, Chichester, Christine, Van Mulligen, Erik, Weeber, Marc, Den Dunnen, Johan, ...
WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from...
Teixeira, Luís, Ferreira, Álvaro, Ashburner, Michael
Wolbachia are vertically transmitted, obligatory intracellular bacteria that infect a great number of species of arthropods and nematodes. In insects, they are mainly known for disrupting the...
FlyBase: enhancing Drosophila Gene Ontology annotations
Tweedie, Susan, Ashburner, Michael, Falls, Kathleen, Leyland, Paul, McQuilton, Peter, Marygold, Steven, ...
FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular...