By: Biospecimen Collection Source Site—NDRI., Biospecimen Collection Source Site—RPCI., Biospecimen Core Resource—VARI., Brain Bank Repository—University of Miami Brain Endowment Bank., Leidos Biomedical—Project Management., ELSI Study., Genome Browser Data Integration &Visualization—EBI., Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz et al. Abstract Characterization …
By: Louis T. Dang, Markus Tondl, Man Ho H. Chiu, Jerico Revote, Benedict Paten, Vincent Tano, Alex Tokolyi, Florence Besse, Greg Quaife-Ryan, Helen Cumming, Mark J. Drvodelic, Michael P. Eichenlaub, Jeannette C. Hallab, Julian S. Stolper, Fernando J. Rossello, Marie A. Bogoyevitch, David A. Jans, Hieu …
By: Shilpa Garg, Mikko Rautiainen, Adam M Novak, Erik Garrison, Richard Durbin, Tobias Marschall Abstract Motivation Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse …
By: Benedict Paten, Jordan M. Eizenga, Yohei M. Rosen, Adam M. Novak, Erik Garrison, and Glenn Hickey Abstract A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genetics, the possible paths through a superbubble can …
By: Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin, Benedict Paten & Richard Durbin Abstract Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references represent only …
By: David Haussler, Maciej Smuga-Otto, Jordan M. Eizenga, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, and Dmitrii Miagkov Abstract Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within …
Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin, Benedict Paten & Richard Durbin Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references represent only one …
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 …
January 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, …
DNA 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 …