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High-throughput microbial population genomics using the Cortex variation assembler

Zamin Iqbal, Isaac Turner, Gil McVean
2012 Computer applications in the biosciences : CABIOS  
We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples.  ...  We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against  ...  Funding: The Wellcome Trust (WT086084/Z/08/Z to G.M.) Conflict of Interest: None declared.  ... 
doi:10.1093/bioinformatics/bts673 pmid:23172865 pmcid:PMC3546798 fatcat:u3i2erlllbahjivn7cqntu533i

Advances and Applications of Single-Cell Sequencing Technologies

Yong Wang, Nicholas E. Navin
2015 Molecular Cell  
Single cell sequencing (SCS) has emerged as a powerful new set of technologies for studying rare cells and delineating complex populations.  ...  In this review, we will discuss SCS technologies and applications, as well as translational applications in the clinic.  ...  This work was also supported by the Moonshot Knowledge Gap Award, the Center for Genetics & Genomics and the Center for Epigenetics at the MD Anderson Cancer Center.  ... 
doi:10.1016/j.molcel.2015.05.005 pmid:26000845 pmcid:PMC4441954 fatcat:ledjl2h36bfo5jluljz2acl3dy

Improved genome inference in the MHC using a population reference graph

Alexander Dilthey, Charles Cox, Zamin Iqbal, Matthew R Nelson, Gil McVean
2015 Nature Genetics  
While much is known about human genetic variation, such information is typically ignored in assembling novel genomes.  ...  We introduce a population reference graph, which combines multiple reference sequences and catalogues of variation.  ...  Summary of read alignment to a single reference (GRCh37 without alternative loci, containing the 'PGF' haplotype in the xMHC) for a single sample (CS1) in the MHC Class II region (around HLA-DRB1) showing  ... 
doi:10.1038/ng.3257 pmid:25915597 pmcid:PMC4449272 fatcat:joascvqf6nh5jpy2pm56j7sxz4

Omics and bioinformatics approaches to target boar taint [article]

Rahul Agarwal, Jitendra Narayan
2016 bioRxiv   pre-print
In livestock species, a rapid growth in high-throughput omics data has accelerated the pace of studies that target to dissect economically important traits to provide better quality animal products to  ...  Existence of porcine reference genome made possible to catalogue genome-wide QTLs, candidate genes and biomarkers in associations with boar taint and other industrially significant traits in pigs.  ...  Assembly of whole genome data was done with help of SOAPdenovo and Cortex genome assemblers. chromosome (BAC) clone libraries.  ... 
doi:10.1101/079301 fatcat:7tb5caw4qrb5lh2bc4kylh6sse

Computational tools for viral metagenomics and their application in clinical research

L. Fancello, D. Raoult, C. Desnues
2012 Virology  
Viral metagenomics, the sequenced-based analysis of the complete collection of viral genomes directly isolated from an organism or an ecosystem, bypasses the "single-organism-level" point of view of clinical  ...  diagnostics and thus the need to isolate and culture the targeted organism.  ...  Acknowledgments This work was funded by a Starting Grant number 242729 from the European Research Council to CD.  ... 
doi:10.1016/j.virol.2012.09.025 pmid:23062738 pmcid:PMC7111993 fatcat:4yys3yeyivebdkkrak4q7rrbxe

The genomic and phenotypic diversity of Schizosaccharomyces pombe

Daniel C Jeffares, Charalampos Rallis, Adrien Rieux, Doug Speed, Martin Převorovský, Tobias Mourier, Francesc X Marsellach, Zamin Iqbal, Winston Lau, Tammy M K Cheng, Rodrigo Pracana, Michael Mülleder (+30 others)
2015 Nature Genetics  
To extend the utility of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates.  ...  We sequenced the genomes of all strains, revealing moderate genetic diversity (π = 3 x10 -3 ) and weak global population structure.  ...  Cells were grown to mid log phase in YES medium and imaged using the OperaLX (PerkinElmer, USA) high-throughput microscope at 60x .  ... 
doi:10.1038/ng.3215 pmid:25665008 pmcid:PMC4645456 fatcat:nnmmaz54sbephik6ax766g6j3m

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)

Matthew Z. DeMaere, Aaron E. Darling
2016 PeerJ  
BackgroundChromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of  ...  Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure.ResultsWhen all genomes in a sample are below 95% sequence identity, all of the  ...  We acknowledge the use of computing resources from the NeCTAR Research Cloud, an Australian Government project conducted as part of the Super Science initiative and supported by the EIF and NCRIS.  ... 
doi:10.7717/peerj.2676 pmid:27843713 pmcid:PMC5103821 fatcat:qrx65y5lq5havn4ya3l7mquqsi

Article Watch: April 2016

Clive A. Slaughter
2016 Journal of Biomolecular Techniques  
The authors apply the methodology, which combines microfluidics, DNA barcoding, and high-throughput sequencing, to the profiling of H3 lysine 4 trimethylation and demethylation in mixed cell populations  ...  The sequence space to be screened is very large, even for small proteins, so screening methods capable of very high throughput are desirable.  ... 
doi:10.7171/jbt.16-2701-006 fatcat:clplu56kn5bj5aencccz5y434a

Panomics for Precision Medicine

Charanjit Sandhu, Alia Qureshi, Andrew Emili
2018 Trends in Molecular Medicine  
High throughput platforms are creating terabytes of genomic, transcriptomic, proteomic and metabolomic data.  ...  variation is accounted for in the treatment of patients.  ...  Acknowledgments AE acknowledges ongoing support as a Research Chair from the Ontario College of Universities, while CS did not receive any specific grant from funding agencies in the public, commercial  ... 
doi:10.1016/j.molmed.2017.11.001 pmid:29217119 pmcid:PMC5839674 fatcat:hhvgssqadrckrdidsis7vjuyyq

Single cell sequencing: a distinct new field

Jian Wang, Yuanlin Song
2017 Clinical and Translational Medicine  
scale of the genome, transcriptome or epigenome at high resolution.  ...  This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and  ...  high-throughput, automation and reliability [106] .  ... 
doi:10.1186/s40169-017-0139-4 pmid:28220395 pmcid:PMC5318355 fatcat:uzf33ozsezg3le737nn6dtqriu

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data [article]

C. Titus Brown, Adina Howe, Qingpeng Zhang, Alexis B. Pyrkosz, Timothy H. Brom
2012 arXiv   pre-print
We apply digital normalization to the assembly of microbial genomic data, amplified single-cell genomic data, and transcriptomic data. Our implementation is freely available for use and modification.  ...  These challenges have led to the development of new classes of mapping tools and de novo assemblers. These algorithms are challenged by the continued improvement in sequencing throughput.  ...  , and Cortex [3, [8] [9] [10] [11] [12] .  ... 
arXiv:1203.4802v2 fatcat:5yb5cbsn7jgxhcmrvvoxac2mvu

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes

Xiaoqing Jiang, Xin Li, Longshu Yang, Chunhong Liu, Qi Wang, Weilai Chi, Huaiqiu Zhu
2019 Genomics, Proteomics & Bioinformatics  
Our study suggests that functional genes are important to the assembly of microbial communities.  ...  In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community.  ...  The genomes of AMD microorganisms were sequenced with high-throughput sequencing strategies [32] .  ... 
doi:10.1016/j.gpb.2018.09.003 pmid:31026577 pmcid:PMC6521236 fatcat:mvibdbvolzco3eddxkmu64lah4

The Theory and Practice of Genome Sequence Assembly

Jared T. Simpson, Mihai Pop
2015 Annual review of genomics and human genetics (Print)  
Here, we survey the key developments in algorithms for assembling genome sequences since the development of the first DNA sequencing methods more than 35 years ago. 153 Annu. Rev. Genom. Hum.  ...  sophisticated computational tools called genome assemblers (short for genome sequence assemblers).  ...  The assembly of high-throughput sequencing data for large genomes would require further algorithmic development, however, because the memory costs of de Bruijn assembly are significant.  ... 
doi:10.1146/annurev-genom-090314-050032 pmid:25939056 fatcat:iayzwkwyljey5nn6hyxhwgsg7u

Building and Improving Reference Genome Assemblies

Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson
2017 Proceedings of the IEEE  
| A genome sequence assembly provides the foundation for studies of genotypic and phenotypic variation, genome structure, and evolution of the target organism.  ...  Here we discuss the relationship between sequencing technology improvements and assembly algorithm development and how these are applied to extend and improve human and nonhuman genome assemblies.  ...  Larson for reading the manuscript and providing comments.  ... 
doi:10.1109/jproc.2016.2645402 fatcat:6mm2qx33fjecxhcbrxnhaebfji

A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease?

Jessica D. Forbes, Charles N. Bernstein, Helen Tremlett, Gary Van Domselaar, Natalie C. Knox
2019 Frontiers in Microbiology  
High-throughput sequencing and computational advancements provide unprecedented ability to investigate the structure and function of microbial communities associated with the human body in health and disease  ...  The human gastrointestinal tract is host to immense populations of microorganisms including bacteria, viruses, archaea, and fungi (the gut microbiota).  ...  genomic DNA content in a sample for high-throughput sequencing.  ... 
doi:10.3389/fmicb.2018.03249 pmid:30687254 pmcid:PMC6333682 fatcat:ni3eralvcjaw3mgkcmxmsxgzuu
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