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High-throughput microbial population genomics using the Cortex variation assembler
2012
Computer applications in the biosciences : CABIOS
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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
2015
Molecular Cell
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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
2015
Nature Genetics
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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]
2016
bioRxiv
pre-print
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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
2012
Virology
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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
2015
Nature Genetics
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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)
2016
PeerJ
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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
2016
Journal of Biomolecular Techniques
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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
2018
Trends in Molecular Medicine
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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
2017
Clinical and Translational Medicine
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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]
2012
arXiv
pre-print
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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
2019
Genomics, Proteomics & Bioinformatics
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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
2015
Annual review of genomics and human genetics (Print)
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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
2017
Proceedings of the IEEE
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| 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?
2019
Frontiers in Microbiology
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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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