Jugmohit S. Too1, imageArjun A. Rao, imageAndrew C. McShan, Mark Yarmarkovich, Santrupti Nerli, Karissa Yamaguchi, Ada A. Madejska, Son Nguyen, Sarvind Tripathi,John M. Maris, Sofie R. Salama, David Haussler, and Nikolaos G. Sgourakis The identification of recurrent human leukocyte antigen (HLA) neoepitopes driving T cell …
Publications
Nanopore sequencing and assembly of a human genome with ultra-long reads
February 7, 2018January 29, 2018 Author: Jain, Miten and Koren, Sergey and Miga, Karen H and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and Malla, Sunir and Marriott, …
Mapping DNA methylation with high-throughput nanopore sequencing
April 10, 2017DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer’s ionic current signal. We map three cytosine variants and two adenine variants. The results show that our model is …
Computational pan-genomics: status, promises and challenges.
October 21, 2016Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply …
Long-read sequence assembly of the gorilla genome
April 11, 2016Improving on the gorilla genome Access to complete, high-quality genomes of nonhuman primates will also help us understand human biology. Gordon et al. used long-read sequencing technology to improve genome data on our close relative the gorilla. Sequencing from a single individual decreased assembly fragmentation …
The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community.
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
March 14, 2016The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing …
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs
January 28, 2016Abstract Background The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich mathematical models. However, it has been observed …
The UCSC Genome Browser database: 2016 update.
November 20, 2015Abstract For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under …
One of the new genome assemblies recently added to the UCSC Genome Browser is the bonobo's.
The UCSC Genome Browser database: 2016 update.
November 20, 2015For the past 15 years, the UCSC Genome Browser has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development …
Matchmaker Exchange to connect databases to speed the research of rare diseases.
The Matchmaker Exchange: A Platform for Rare Disease Discovery.
October 30, 2015There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for “the needle in a haystack” to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery …