Local read haplotagging enables accurate long-read small variant calling

Autor: Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John Gorzynski, Sneha Goenka, Euan A. Ashley, Miten Jain, Karen H. Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)

Abstract Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences

Externí odkaz: https://doaj.org/article/9736ff93823742a28239875aa6195f95

Inversion polymorphism in a complete human genome assembly

Autor: David Porubsky, William T. Harvey, Allison N. Rozanski, Jana Ebler, Wolfram Höps, Hufsah Ashraf, Patrick Hasenfeld, Human Pangenome Reference Consortium (HPRC), Human Genome Structural Variation Consortium (HGSVC), Benedict Paten, Ashley D. Sanders, Tobias Marschall, Jan O. Korbel, Evan E. Eichler

Publikováno v: Genome Biology, Vol 24, Iss 1, Pp 1-16 (2023)

Abstract The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we remapped data from 41 genomes against the T2T

Externí odkaz: https://doaj.org/article/255e9b3d13f44bcfa4cd688e4f4d79ba

Bridging the rodent to human translational gap: Marmosets as model systems for the study of Alzheimer's disease

Autor: Stacey J. Sukoff Rizzo, Gregg Homanics, David J. Schaeffer, Lauren Schaeffer, Jung Eun Park, Julia Oluoch, Tingting Zhang, Annat Haber, Nicholas T. Seyfried, Benedict Paten, Anna Greenwood, Takeshi Murai, Sang Ho Choi, Hasi Huhe, Julia Kofler, Peter L. Strick, Gregory W. Carter, Afonso C. Silva

Publikováno v: Alzheimer’s & Dementia: Translational Research & Clinical Interventions, Vol 9, Iss 3, Pp n/a-n/a (2023)

Abstract Introduction Our limited understanding of the mechanisms that trigger the emergence of Alzheimer's disease (AD) has contributed to the lack of interventions that stop, prevent, or fully treat this disease. We believe that the development of

Externí odkaz: https://doaj.org/article/6c07eec0388e40f586e42c6bf6451b34

Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

Autor: Andrew D Bailey, Jason Talkish, Hongxu Ding, Haller Igel, Alejandra Duran, Shreya Mantripragada, Benedict Paten, Manuel Ares

Publikováno v: eLife, Vol 11 (2022)

Nucleotides in RNA and DNA are chemically modified by numerous enzymes that alter their function. Eukaryotic ribosomal RNA (rRNA) is modified at more than 100 locations, particularly at highly conserved and functionally important nucleotides. During

Externí odkaz: https://doaj.org/article/c4e021b69ec44e9c831496f959d90b0b

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Autor: Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L. Grossman, Ira M. Hall, Kasper D. Hansen, Jonathan Lawson, Jeffrey T. Leek, Anne O’Donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D. O’Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J. Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet, Alexander Baumann, Andrew Rula, Anton Kovalsy, Clare Bernard, Derek Caetano-Anollés, Geraldine A. Van der Auwera, Justin Canas, Kaan Yuksel, Kate Herman, M. Morgan Taylor, Marianie Simeon, Michael Baumann, Qi Wang, Robert Title, Ruchi Munshi, Sushma Chaluvadi, Valerie Reeves, William Disman, Salin Thomas, Allie Hajian, Elizabeth Kiernan, Namrata Gupta, Trish Vosburg, Ludwig Geistlinger, Marcel Ramos, Sehyun Oh, Dave Rogers, Frances McDade, Mim Hastie, Nitesh Turaga, Alexander Ostrovsky, Alexandru Mahmoud, Dannon Baker, Dave Clements, Katherine E.L. Cox, Keith Suderman, Nataliya Kucher, Sergey Golitsynskiy, Samantha Zarate, Sarah J. Wheelan, Kai Kammers, Ana Stevens, Carolyn Hutter, Christopher Wellington, Elena M. Ghanaim, Ken L. Wiley, Jr., Shurjo K. Sen, Valentina Di Francesco, Deni s Yuen, Brian Walsh, Luke Sargent, Vahid Jalili, John Chilton, Lori Shepherd, B.J. Stubbs, Ash O’Farrell, Benton A. Vizzier, Jr., Charles Overbeck, Charles Reid, David Charles Steinberg, Elizabeth A. Sheets, Julian Lucas, Lon Blauvelt, Louise Cabansay, Noah Warren, Brian Hannafious, Tim Harris, Radhika Reddy, Eric Torstenson, M. Katie Banasiewicz, Haley J. Abel, Jason Walker

Publikováno v: Cell Genomics, Vol 2, Iss 1, Pp 100085- (2022)

Summary: The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, managemen

Externí odkaz: https://doaj.org/article/95ac1623e901491c821d128f529da364