Zobrazeno 1 - 10
of 110
pro vyhledávání: '"Ben, Langmead"'
Autor:
Li Song, Ben Langmead
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-21 (2024)
Abstract Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the Burrows-Wheeler transformed genome sequences are losslessly compressed using a novel scheme c
Externí odkaz:
https://doaj.org/article/5be3381339a04fabb1c14e1cb01f84ee
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-28 (2024)
Abstract Many bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it. Biastools analyzes and categorizes instances of reference bias. It works in various scenarios: when the donor’s variants are kno
Externí odkaz:
https://doaj.org/article/c936d679c84f4a0e8c5983cd97575663
Autor:
Anna-Maria Liebhoff, Thiagarajan Venkataraman, William R. Morgenlander, Miso Na, Tomasz Kula, Kathleen Waugh, Charles Morrison, Marian Rewers, Randy Longman, June Round, Stephen Elledge, Ingo Ruczinski, Ben Langmead, H. Benjamin Larman
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)
Abstract We investigate a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To cover large antigenic spaces, we develop Dolphyn, a method
Externí odkaz:
https://doaj.org/article/f671256a5dbb468ba920e54a8c3dd8ac
Publikováno v:
iScience, Vol 27, Iss 3, Pp 109054- (2024)
Summary: Genome assembly databases are growing rapidly. The redundancy of sequence content between a new assembly and previous ones is neither conceptually nor algorithmically easy to measure. We introduce pertinent methods and DandD, a tool addressi
Externí odkaz:
https://doaj.org/article/6e8f3a7b02ad4b949bc660f167539911
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-15 (2023)
Abstract Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a novel
Externí odkaz:
https://doaj.org/article/beed168329644a80b28abeb68de43d92
Publikováno v:
Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-17 (2023)
Abstract We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the mark
Externí odkaz:
https://doaj.org/article/888f8695e03e43e9ba63a8ffe3afb45d
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-14 (2023)
Abstract Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, availability of these data
Externí odkaz:
https://doaj.org/article/7e968b6a62e94e5794bc75f7fce5eadb
Autor:
Jonathan P. Ling, Alexei M. Bygrave, Clayton P. Santiago, Rogger P. Carmen-Orozco, Vickie T. Trinh, Minzhong Yu, Yini Li, Ying Liu, Kyra D. Bowden, Leighton H. Duncan, Jeong Han, Kamil Taneja, Rochinelle Dongmo, Travis A. Babola, Patrick Parker, Lizhi Jiang, Patrick J. Leavey, Jennifer J. Smith, Rachel Vistein, Megan Y. Gimmen, Benjamin Dubner, Eric Helmenstine, Patric Teodorescu, Theodoros Karantanos, Gabriel Ghiaur, Patrick O. Kanold, Dwight Bergles, Ben Langmead, Shuying Sun, Kristina J. Nielsen, Neal Peachey, Mandeep S. Singh, W. Brian Dalton, Fatemeh Rajaii, Richard L. Huganir, Seth Blackshaw
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-14 (2022)
Precise and reliable gene delivery remains technically challenging. Here, the authors show that rationally designed frameshifting splicing can be used to express genes only in targeted cell types, with the potential to enhance the specificity AAV gen
Externí odkaz:
https://doaj.org/article/d3c897c79c354a7aba8f34a9159e9fad
Publikováno v:
iScience, Vol 26, Iss 8, Pp 107402- (2023)
Summary: A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenom
Externí odkaz:
https://doaj.org/article/2a6484f345c243dab7f5c716214b5895
Autor:
Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D. Hansen, Ben Langmead
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-40 (2021)
Abstract We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recoun
Externí odkaz:
https://doaj.org/article/8ffd406a24644e9286dbf6b7448b3e96