By: Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert …
Publications
Genetic effects on gene expression across human tissues.
October 5, 2018By: 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 …
TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets
October 5, 2018By: 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 …
A graph-based approach to diploid genome assembly
October 5, 2018By: 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 …
Superbubbles, Ultrabubbles, and Cacti.
October 5, 2018By: 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 …
Variation graph toolkit improves read mapping by representing genetic variation in the reference
October 5, 2018By: 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 …
A Flow Procedure for Linearization of Genome Sequence Graphs
October 5, 2018By: 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 …
Variation graph toolkit improves read mapping by representing genetic variation in the reference
August 28, 2018Erik 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 …
A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations
February 13, 2018Jugmohit 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 …
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, …