{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T00:12:15Z","timestamp":1759104735660},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2220,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u00a0De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria.<\/jats:p>\n               <jats:p>Results: The developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN.PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp; a drastic improvement compared with the single assemblies.<\/jats:p>\n               <jats:p>Availability: MAIA is available as a Matlab package and can be downloaded from http:\/\/bioinformatics.tudelft.nl<\/jats:p>\n               <jats:p>Contact: \u00a0j.f.nijkamp@tudelft.nl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq366","type":"journal-article","created":{"date-parts":[[2010,9,7]],"date-time":"2010-09-07T17:41:46Z","timestamp":1283881306000},"page":"i433-i439","source":"Crossref","is-referenced-by-count":34,"title":["Integrating genome assemblies with MAIA"],"prefix":"10.1093","volume":"26","author":[{"given":"Jurgen","family":"Nijkamp","sequence":"first","affiliation":[{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"}]},{"given":"Wynand","family":"Winterbach","sequence":"additional","affiliation":[{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"}]},{"given":"Marcel","family":"van den Broek","sequence":"additional","affiliation":[{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"}]},{"given":"Jean-Marc","family":"Daran","sequence":"additional","affiliation":[{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"}]},{"given":"Marcel","family":"Reinders","sequence":"additional","affiliation":[{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"}]},{"given":"Dick","family":"de Ridder","sequence":"additional","affiliation":[{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"},{"name":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Industrial Microbiology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, 4Network Architectures and Services, Department of Telecommunications, Delft University of Technology, Mekelweg 4, 2628 CD Delft and 5Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2010,9,4]]},"reference":[{"key":"2023012508222648100_B1","doi-asserted-by":"crossref","first-page":"2258","DOI":"10.1101\/gr.091777.109","article-title":"Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production","volume":"19","author":"Argueso","year":"2009","journal-title":"Genome Res."},{"key":"2023012508222648100_B2","volume-title":"Methods in Yeast Genetics: a Cold Spring Harbor Laboratory Course Manual.","author":"Burke","year":"2000"},{"key":"2023012508222648100_B3","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1093\/nar\/30.11.2478","article-title":"Fast algorithms for large-scale genome alignment and comparison","volume":"30","author":"Delcher","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012508222648100_B4","doi-asserted-by":"crossref","first-page":"R94","DOI":"10.1186\/gb-2009-10-9-r94","article-title":"De novo genome sequence assembly of a filamentous fungus using sanger, 454 and illumina sequence data","volume":"10","author":"Diguistini","year":"2009","journal-title":"Genome Biol."},{"key":"2023012508222648100_B5","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/0305-0548(86)90048-1","article-title":"Future paths for integer programming and links to artificial intelligence","volume":"13","author":"Glover","year":"1986","journal-title":"Comput. 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