Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens
The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pip...
| Main Authors: | , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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BioMed Central Ltd
2014
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| Online Access: | http://hdl.handle.net/1721.1/92385 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1811088800960479232 |
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| author | Abbey, Darren A. Funt, Jason Lurie-Weinberger, Mor N. Thompson, Dawn A. Regev, Aviv Myers, Chad L. Berman, Judith |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Abbey, Darren A. Funt, Jason Lurie-Weinberger, Mor N. Thompson, Dawn A. Regev, Aviv Myers, Chad L. Berman, Judith |
| author_sort | Abbey, Darren A. |
| collection | MIT |
| description | The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans, the most prevalent human fungal pathogen. The Y[subscript MAP] pipeline (http://lovelace.cs.umn.edu/Ymap/) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes. |
| first_indexed | 2024-09-23T14:07:45Z |
| format | Article |
| id | mit-1721.1/92385 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:07:45Z |
| publishDate | 2014 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/923852022-10-01T19:22:22Z Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens Y[subscript MAP]: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens Abbey, Darren A. Funt, Jason Lurie-Weinberger, Mor N. Thompson, Dawn A. Regev, Aviv Myers, Chad L. Berman, Judith Massachusetts Institute of Technology. Department of Biology Regev, Aviv The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans, the most prevalent human fungal pathogen. The Y[subscript MAP] pipeline (http://lovelace.cs.umn.edu/Ymap/) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes. Howard Hughes Medical Institute Burroughs Wellcome Fund (Career Award at the Scientific Interface) National Institutes of Health (U.S.) (PIONEER Award) Alfred P. Sloan Foundation (Fellowship) National Institute of Allergy and Infectious Diseases (U.S.) (R01 AI-0624273) 2014-12-18T18:36:27Z 2014-12-18T18:36:27Z 2014-11 2014-07 2014-12-11T20:54:42Z Article http://purl.org/eprint/type/JournalArticle 1756-994X http://hdl.handle.net/1721.1/92385 Abbey, Darren A, et al., “Y MAP: a Pipeline for Visualization of Copy Number Variation and Loss of Heterozygosity in Eukaryotic Pathogens.” Genome Medicine 6, no. 11 (2014): 100. https://orcid.org/0000-0001-8567-2049 en http://dx.doi.org/10.1186/s13073-014-0100-8 Genome Medicine Creative Commons Attribution http://creativecommons.org/licenses/by/4.0 Darren A Abbey et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Abbey, Darren A. Funt, Jason Lurie-Weinberger, Mor N. Thompson, Dawn A. Regev, Aviv Myers, Chad L. Berman, Judith Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens |
| title | Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens |
| title_full | Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens |
| title_fullStr | Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens |
| title_full_unstemmed | Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens |
| title_short | Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens |
| title_sort | y map a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens |
| url | http://hdl.handle.net/1721.1/92385 https://orcid.org/0000-0001-8567-2049 |
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