User profiles for Jared T Simpson
Jared SimpsonOntario Institute for Cancer Research Verified email at oicr.on.ca Cited by 39632 |
ABySS: a parallel assembler for short read sequence data
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing
instruments has prompted the recent development of de novo short read assembly algorithms. A …
instruments has prompted the recent development of de novo short read assembly algorithms. A …
[HTML][HTML] Nanopore sequencing and assembly of a human genome with ultra-long reads
We report the sequencing and assembly of a reference genome for the human GM12878
Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. …
Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. …
Real-time, portable genome sequencing for Ebola surveillance
The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over
28,599 cases and more than 11,299 deaths 1 . Genome sequencing in viral outbreaks is …
28,599 cases and more than 11,299 deaths 1 . Genome sequencing in viral outbreaks is …
Shotgun metagenomics, from sampling to analysis
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are frequently …
have crucial roles in the environment and in human health. However, microbes are frequently …
A complete bacterial genome assembled de novo using only nanopore sequencing data
We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb
contig using only nanopore data. Our method has three stages: (i) overlaps are …
contig using only nanopore data. Our method has three stages: (i) overlaps are …
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
…, SA Baylis, NR Faria, M Loose, JT Simpson… - Nature protocols, 2017 - nature.com
Genome sequencing has become a powerful tool for studying emerging infectious diseases;
however, genome sequencing directly from clinical samples (ie, without isolation and culture…
however, genome sequencing directly from clinical samples (ie, without isolation and culture…
Complex landscapes of somatic rearrangement in human breast cancer genomes
Multiple somatic rearrangements are often found in cancer genomes; however, the underlying
processes of rearrangement and their contribution to cancer development are poorly …
processes of rearrangement and their contribution to cancer development are poorly …
Efficient de novo assembly of large genomes using compressed data structures
JT Simpson, R Durbin - Genome research, 2012 - genome.cshlp.org
De novo genome sequence assembly is important both to generate new sequence
assemblies for previously uncharacterized genomes and to identify the genome sequence of …
assemblies for previously uncharacterized genomes and to identify the genome sequence of …
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
…, G Harden, T Hubbard, S Pelan, JT Simpson… - Genome …, 2017 - genome.cshlp.org
The human reference genome assembly plays a central role in nearly all aspects of today's
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …
[HTML][HTML] Insights into hominid evolution from the gorilla genome sequence
…, S Sajjadian, D Schmidt, K Shaw, JT Simpson… - Nature, 2012 - nature.com
Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable
importance for the study of human origins and evolution. Here we present the assembly and …
importance for the study of human origins and evolution. Here we present the assembly and …