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Ian Longden

Bio: Ian Longden is an academic researcher from Wellcome Trust. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 2, co-authored 2 publications receiving 9001 citations.
Topics: Medicine, Biology, Genome, Model organism, UniProt

Papers
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Journal ArticleDOI
TL;DR: The European Molecular Biology Open Software Suite is a mature package of software tools developed for the molecular biology community that includes a comprehensive set of applications for molecular sequence analysis and other tasks and integrates popular third-party software packages under a consistent interface.

9,493 citations

Journal ArticleDOI
TL;DR: FPC is an integrated program for the assembly of sequence-ready clones for large-scale sequencing projects and uses an algorithm to cluster clones into contigs based on their probability of coincidence score.
Abstract: Motivation: To meet the demands of large-scale sequencing, thousands of clones must be fingerprinted and assembled into contigs. To determine the order of clones, a typical experiment is to digest the clones with one or more restriction enzymes and measure the resulting fragments. The probability of two clones overlapping is based on the similarity of their fragments. A contig contains two or more overlapping clones and a minimal tiling path of clones is selected to be sequenced. Interactive software with algorithmic support is necessary to assemble the clones into contigs quickly. Results: FPC (fingerprinted contigs) is an interactive program for building contigs from restriction fingerprinted clones. FPC uses an algorithm to cluster clones into contigs based on their probability of coincidence score. For each contig, it builds a consensus band (CB) map which is similar to a restriction map, but it does not try to resolve all the errors. The CB map is used to assign coordinates to the clones based on their alignment to the map and to provide a detailed visualization of the clone overlap. FPC has editing facilities for the user to refine the coordinates and to remove poorly fingerprinted clones. Functions are available for updating an FPC database with new clones. Contigs can easily be merged, split or deleted. Markers can be added to clones and are displayed with the appropriate contig. Sequence-ready clones can be selected and their sequencing status displayed. As such, FPC is an integrated program for the assembly of sequence-read y clones for large-scale sequencing projects. Availability: The software and manual are available via anonymous ftp toftp.sanger.ac.uk, directory publfpc.

304 citations

Journal ArticleDOI
10 Mar 2022-Genetics
TL;DR: FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster, and the dedicated reports and tools it has constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities are emphasized.
Abstract: Abstract FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.

126 citations

Journal ArticleDOI
Julie Agapite, Laurent-Philippe Albou, Suzanne A. Aleksander, Micheal Alexander, Anna V Anagnostopoulos, Giulia Antonazzo, Joanna Gdula Argasinska, Valerio Arnaboldi, Helen Attrill, Andres Andrade Becerra, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jaeyoung Choi, Karen R. Christie, Madeline A. Crosby, Paul H. Davis, Eduardo da Veiga Beltrame, Jeff De Pons, Peter D'Eustachio, Stavros Diamantakis, M. Eileen Dolan, Gilberto dos Santos, Eric Douglass, Barbara Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Stephen F. Foley, K. S. Frazer, Sibyl Gao, A. C. Gibson, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Paul Hale, Todd W. Harris, G. Thomas Hayman, David J. Hill, Doug Howe, Kevin L. Howe, Yan Mengand Qiao-Mu Hu, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Anne E. Kwitek, Stan Laulederkind, Raymond Lee, Ian Longden, Manuel Luypaert, Kevin A. MacPherson, Ryan Martin, Steven J Marygold, Beverley B. Matthews, Monica S. McAndrews, Gillian Millburn, Stuart R. Miyasato, Howie Motenko, Sierra A. T. Moxon, Hans Michael Muller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Harika S Nalabolu, Robert S. Nash, Patrick Ng, Paulo A. S. Nuin, Holly Paddock, Michael Paulini, Norbert Perrimon, Christian Pich, Mark Quinton-Tulloch, Daniela Raciti, Sridhar Ramachandran, Joel E. Richardson, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Gary Schindelman, Mary Shimoyama, Matt Simison, David R. Shaw, Ajay Shrivatsav, Amy Singer, Marek S. Skrzypek, Constance M. Smith, Cynthia L. Smith, Lincoln Stein, Paul W. Sternberg, Christopher J. Tabone, Paul Thomas, K. Thorat, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Vítor Trovisco, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Qinghua Wang, Shur-Jen Wang, Shuai Wang, Monte Westerfield, Gary Williams, Laurens G. Wilming, Edith D. Wong, Adam Wright, Karen Yook, Magdalena Zarowiecki, Pinglei Zhou, Mark Zytkovicz 
25 Feb 2022-Genetics
TL;DR: The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance and expects other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.
Abstract: Abstract The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

37 citations


Cited by
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Journal ArticleDOI
Eric S. Lander1, Lauren Linton1, Bruce W. Birren1, Chad Nusbaum1  +245 moreInstitutions (29)
15 Feb 2001-Nature
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

22,269 citations

Journal ArticleDOI
TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
Abstract: When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/

20,255 citations

Journal ArticleDOI
TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Abstract: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence. le formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.

3,855 citations

Journal ArticleDOI
TL;DR: Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis and provide support for capturing the context and intent of computational methods.
Abstract: Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.

3,576 citations

Journal ArticleDOI
TL;DR: It is shown that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment.
Abstract: The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.

3,535 citations