Y MAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

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...

Full description

Bibliographic Details
Main Authors:	Abbey, Darren A. (Author), Funt, Jason (Author), Lurie-Weinberger, Mor N. (Author), Thompson, Dawn A. (Author), Regev, Aviv (Contributor), Myers, Chad L. (Author), Berman, Judith (Author)
Other Authors:	Massachusetts Institute of Technology. Department of Biology (Contributor)
Format:	Article
Language:	English
Published:	BioMed Central Ltd, 2014-12-18T18:36:27Z.
Subjects:	Article
Online Access:	Get fulltext

Similar Items

Somatic copy-neutral loss of heterozygosity and copy number abnormalities in Malaysian sporadic colorectal carcinoma patients
by: Ankathil, R, et al.

Loss of heterozygosity and copy number alterations in flow-sorted bulky cervical cancer.
by: Sabrina A H M van den Tillaart, et al.
Published: (2013-01-01)

Probabilistic approaches for profiling copy number aberrations and loss of heterozygosity landscapes in cancer genomes
by: Ha, Gavin
Published: (2014)

Genetic Diversity of the Flavohemoprotein Gene of Giardia lamblia: Evidence for High Allelic Heterozygosity and Copy Number Variation
by: Saghaug CS, et al.
Published: (2020-12-01)

Genome-Wide Analysis of DNA Copy Number Alterations and Loss of Heterozygosity in Intracranial Germ Cell Tumors
by: 寺島, 慶太, et al.
Published: (2013)

Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification.
by: Angela Stokes, et al.
Published: (2011-01-01)

Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma
by: Ding Ti, et al.
Published: (2010-10-01)

Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival.
by: Chu Chen, et al.
Published: (2015-01-01)

Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array
by: Goldstein Alisa M, et al.
Published: (2006-11-01)

R-Gada: a fast and flexible pipeline for copy number analysis in association studies
by: Cáceres Alejandro, et al.
Published: (2010-07-01)

Estimation of 18S Gene Copy Number in Marine Eukaryotic Plankton Using a Next-Generation Sequencing Approach
by: Weida Gong, et al.
Published: (2019-04-01)

Fungal regulatory evolution: cis and trans in the balance
by: Thompson, Dawn Anne, et al.
Published: (2012)

Loss of Heterozygosity and Copy Number Abnormality in Clear Cell Renal Cell Carcinoma Discovered by High-Density Affymetrix 10K Single Nucleotide Polymorphism Mapping Array
by: Marieta I. Toma, et al.
Published: (2008-07-01)

SNP array analysis reveals novel genomic abnormalities including copy neutral loss of heterozygosity in anaplastic oligodendrogliomas.
by: Ahmed Idbaih, et al.
Published: (2012-01-01)

Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays
by: Cowell John K, et al.
Published: (2008-10-01)

CRISPR-Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells
by: J. Boutin, et al.
Published: (2021-08-01)

Correction: SNP Array Analysis Reveals Novel Genomic Abnormalities Including Copy Neutral Loss of Heterozygosity in Anaplastic Oligodendrogliomas
by: Ahmed Idbaih, et al.
Published: (2013-01-01)

Correction: SNP Array Analysis Reveals Novel Genomic Abnormalities Including Copy Neutral Loss of Heterozygosity in Anaplastic Oligodendrogliomas.
by: Ahmed Idbaih, et al.
Published: (2013-01-01)

The evolution of drug resistance in clinical isolates of Candida albicans
by: Christopher B Ford, et al.
Published: (2015-02-01)

The evolution of drug resistance in clinical isolates of Candida albicans
by: Abbey, Darren A., et al.
Published: (2015)

A new method to detect loss of heterozygosity using cohort heterozygosity comparisons
by: Lea Rod A, et al.
Published: (2010-05-01)

A Pipeline for Reconstructing Somatic Copy Number Alternation’s Subclonal Population-Based Next-Generation Sequencing Data
by: Yanshuo Chu, et al.
Published: (2020-02-01)

Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data
by: Jianing Gao, et al.
Published: (2017-10-01)

Genome-wide detection of loss of heterozygosity and copy number variation in a human lung large cell carcinoma cell line by affymetrix single-nucleotide polymorphism array 500K
by: Bin HU, et al.
Published: (2008-06-01)

Archaea in and on the Human Body: Health Implications and Future Directions.
by: Mor N Lurie-Weinberger, et al.
Published: (2015-06-01)

A single-cell genomics pipeline for environmental microbial eukaryotes
by: Doina Ciobanu, et al.
Published: (2021-04-01)

Copy neutral absence of heterozygosity on chromosome 15 distal long arm: A surrogate marker for Prader–Willi/Angelman syndromes?
by: Veronica Ortega, et al.
Published: (2021-07-01)

Copy Number Analysis of Cancer
by: Mayrhofer, Markus
Published: (2015)

Copy number variation and schizophrenia
by: Tam, Gloria Wing Chi
Published: (2009)

Copy number variation in familial Parkinson disease.
by: Nathan Pankratz, et al.
Published: (2011-01-01)

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
by: de Boer, Carl G, et al.
Published: (2020)

HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts
by: Soukaina Timouma, et al.
Published: (2020-10-01)

Genetic association studies of copy-number variation: should assignment of copy number states precede testing?
by: Patrick Breheny, et al.
Published: (2012-01-01)

The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility
by: Fabrizio Signore, et al.
Published: (2019-12-01)

Comparing copy-number profiles under multi-copy amplifications and deletions
by: Garance Cordonnier, et al.
Published: (2020-04-01)

Does MHC heterozygosity influence microbiota form and function?
by: M A Wadud Khan, et al.
Published: (2019-01-01)

Uniparental isodisomy caused autosomal recessive diseases: NGS‐based analysis allows the concurrent detection of homogenous variants and copy‐neutral loss of heterozygosity
by: Bing Xiao, et al.
Published: (2019-10-01)

Genomic copy number variation in schizophrenia
by: Rudd, Danielle Song
Published: (2014)

Copy number variation in African Americans
by: Caillier Stacy J, et al.
Published: (2009-03-01)

Copy number variation in Thai population.
by: Bhoom Suktitipat, et al.
Published: (2014-01-01)