A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference
[article]
2016
bioRxiv
pre-print
Preserved Fulltext
We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional 'reference genome', incorporating ...
Our goal is to support the inference of the closest mosaic of previously known sequences to the genome(s) under analysis. ...
We would like to thank Jacob Almagro-Garcia, Phelim Bradley, Rayan Chikhi, Simon Gog, Lin Huang, Jerome Kelleher, Heng Li, Gerton Lunter, Rachel Norris, Victoria Popic, and Jouni Siren for discussions ...
doi:10.1101/059170
fatcat:y75zskexsbgyjo62cfukdtwhd4
A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference
[chapter]
2016
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional "reference genome", incorporating ...
Our goal is to support the inference of the closest mosaic of previously known sequences to the genome(s) under analysis. ...
We would like to thank Jacob Almagro-Garcia, Phelim Bradley, Rayan Chikhi, Simon Gog, Lin Huang, Jerome Kelleher, Heng Li, Gerton Lunter, Rachel Norris, Victoria Popic, and Jouni Siren for discussions ...
doi:10.1007/978-3-319-43681-4_18
fatcat:kiksaij2s5ashhypn75sj64pyi
An improved encoding of genetic variation in a Burrows-Wheeler transform
[article]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
In a different approach, Maciuca et al. (2016) provided a 'natural encoding' of SNPs and other genetic variations in a BWT. ...
Currently dominant read mappers (Li and Durbin, 2009; Langmead and Salzberg, 2012) are based on the Burrows-Wheeler transform (BWT). ...
Discussion We have presented a new method to encode genetic variation in a Burrows-Wheeler transform, which extends the work of Huang et al. (2013) and Maciuca et al. (2016) in several aspects. ...
doi:10.1101/658716
fatcat:7govp2jpwfe4bjxs5f3qdq4ypi
Computational pan-genomics: status, promises and challenges
2016
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
In this article, we generalize existing definitions and understand a pangenome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. ...
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. ...
In particular, we like to thank the Lorentz Center staff, who turned organizing and attending the workshop into a great pleasure. ...
doi:10.1093/bib/bbw089
pmid:27769991
pmcid:PMC5862344
fatcat:zeeomxopezehvl44bnap76snyq
Computational Pan-Genomics: Status, Promises and Challenges
[article]
2016
biorxiv/medrxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
In this paper, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. ...
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. ...
There is also a special Burrows-Wheeler transform and an index based on that for a sequence graph [132, 133] . ...
doi:10.1101/043430
fatcat:fhuu62lklndwtgct7d6qvxlsoi
Sensitive and fast mapping of di-base encoded reads
2011
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Motivation: Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads. ...
, including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold. ...
Funding: Natural Sciences and Engineering Research Council of Canada (NSERC to S.C.S. in parts); Bioinformatics for Combating Infectious Diseases (BCID to S.C.S. in parts); Michael Smith Foundation for ...
doi:10.1093/bioinformatics/btr303
pmid:21586516
pmcid:PMC3129524
fatcat:3pl3auezdbcg7hl7q6rlizptoe
Sensitive and fast mapping of di-base encoded reads
2011
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Motivation: Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads. ...
, including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold. ...
Funding: Natural Sciences and Engineering Research Council of Canada (NSERC to S.C.S. in parts); Bioinformatics for Combating Infectious Diseases (BCID to S.C.S. in parts); Michael Smith Foundation for ...
doi:10.1093/bioinformatics/btr647
pmcid:PMC3276229
fatcat:rhah2ss57nbnlnahei4vubil5y
Genome graphs and the evolution of genome inference
2017
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We thank David Haussler, Richard Durbin, Gil McVean, and members of the reference-genomes task team of the Global Alliance for Genomics and Health for many useful discussions. ...
We thank Glenn Hickey, Charles Markello, Yohei Rosen, Eric Dawson, Mike Lin, and all contributors to the vg software package, which is driving much of our work forward. ...
In linear references, the Positional Burrows-Wheeler Transform (PBWT) was developed in response to this challenge. ...
doi:10.1101/gr.214155.116
pmid:28360232
pmcid:PMC5411762
fatcat:hnzivagd3vef5jro7dsyc55eky
Graphical Pangenomics
2018
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large. ...
As this model combines both sequence and variation information in one structure it serves as a natural basis for resequencing. ...
the Burrows-Wheeler Transform (BWT) [28] . ...
doi:10.5281/zenodo.1463032
fatcat:e65awps6hbav5gczb3ubrf65oi
Graphical pangenomics
2018
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large. ...
As this model combines both sequence and variation information in one structure it serves as a natural basis for resequencing. ...
sibling the Burrows-Wheeler Transform (BWT) [28] . ...
doi:10.5281/zenodo.3269840
fatcat:glracsk2jvgb3lehvepq2jl5l4
Computational solutions for omics data
2013
Nature reviews genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Fortunately, an arsenal of algorithmic ideasapplicable in a wide variety of biological settings -can be deployed to address these challenges. ...
In the past two decades, improvements in genomic sequencing capability have led to an exponential growth in the amount of publicly available sequence data that far outstrips the ...
Acknowledgments The authors thank and L. Cowen for valuable feedback. B.B. thanks the US National Institutes of Health (NIH) for grant GM081871. ...
doi:10.1038/nrg3433
pmid:23594911
pmcid:PMC3966295
fatcat:b7n6xwzyc5gqzo7plgyoe257iq
Complex modifier landscape underlying genetic background effects
2019
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Here, in addition to confirming that some conditional essential genes are modified by a nonchromosomal element, we show that most cases involve a complex set of genomic modifiers. ...
In natural yeast isolates, we found that the CYS3/CYS4 conditional essentiality can be caused by variation in two independent modifiers, MET1 and OPT1, each with roles associated with cellular cysteine ...
The authors declare no conflict of interest. ...
doi:10.1073/pnas.1820915116
fatcat:7qcuxjentzajnddsdtdgcjara4
Genome Graphs and the Evolution of Genome Inference
[article]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Here, we survey various projects underway to build and apply these graph based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling, ...
However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. ...
Disclosure Declaration The authors of this manuscript include authors of the vg Garrison (2016) and Glia tools described above. The authors declare no other conflicts of interest. ...
doi:10.1101/101816
fatcat:2kpmyq4fvfhdzjrgeegduufoky
Inferring whole-genome histories in large population datasets
2019
Nature Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Inferring the full genealogical history of a set of DNA sequences is a core problem in evolutionary biology, because this history encodes information about the events and forces that have influenced a ...
We apply the method to human data from the 1000 Genomes Project, Simons Genome Diversity Project and UK Biobank, showing that the inferred genealogies are rich in biological signal and efficient to process ...
Computation used the Oxford Biomedical Research Computing (BMRC) facility, a joint development between the Wellcome Centre for Human Genetics and the Big Data Institute supported by Health Data Research ...
doi:10.1038/s41588-019-0483-y
pmid:31477934
pmcid:PMC6726478
fatcat:kjs5lushcrfjbikx5glygf2why
Reference-based phasing using the Haplotype Reference Consortium panel
2016
Nature Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Reference Consortium, HRC) using a new data structure based on the positional Burrows-Wheeler transform. ...
Haplotype phasing is a fundamental problem in medical and population genetics. ...
(a) We use the positional Burrows-Wheeler transform[19] to generate a "hedge" of haplotype prefix trees rooted at markers spaced across the chromosome. ...
doi:10.1038/ng.3679
pmid:27694958
pmcid:PMC5096458
fatcat:ojaubddehfga3chlly7tkzmd2y
« Previous
Showing results 1 — 15 out of 593 results