Zobrazeno 1 - 10
of 358
pro vyhledávání: '"Carl Kingsford"'
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-24 (2024)
Abstract The graph traversal edit distance (GTED), introduced by Ebrahimpour Boroojeny et al. (2018), is an elegant distance measure defined as the minimum edit distance between strings reconstructed from Eulerian trails in two edge-labeled graphs. G
Externí odkaz:
https://doaj.org/article/8be5fffc7ce74715b158837f4477ac5f
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-25 (2021)
Abstract Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic va
Externí odkaz:
https://doaj.org/article/704b27b4a9634b5ca4dd152c991eb668
Publikováno v:
Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-15 (2021)
Abstract Background The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts. We call this model graph quantification, wh
Externí odkaz:
https://doaj.org/article/3aa32f8e04cf4d65a2f332686ae4d0ae
Autor:
Trevor S. Frisby, Shawn J. Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford, Christopher J. Langmead
Publikováno v:
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-19 (2021)
Abstract Background Supervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to overfitting as well as issues with scalability. This can bring about inaccurate models or those
Externí odkaz:
https://doaj.org/article/1fc059f1c09743c3894a51417a32d3cc
Autor:
Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-29 (2020)
Abstract Background The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been
Externí odkaz:
https://doaj.org/article/78912e03065e4f5e8d496ea17a6e5ae8
Publikováno v:
Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-12 (2020)
Abstract Motivation Most modern seed-and-extend NGS read mappers employ a seeding scheme that requires extracting t non-overlapping seeds in each read in order to find all valid mappings under an edit distance threshold of t. As t grows, this seeding
Externí odkaz:
https://doaj.org/article/78746fdbfe3845f38d771556712751e1
Publikováno v:
Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-15 (2020)
Abstract Background Transcriptomic structural variants (TSVs)—large-scale transcriptome sequence change due to structural variation - are common in cancer. TSV detection from high-throughput sequencing data is a computationally challenging problem.
Externí odkaz:
https://doaj.org/article/582d03c624724f7fbc489091978dfd9d
Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads
Publikováno v:
Genome Biology, Vol 20, Iss 1, Pp 1-18 (2019)
Abstract Single-molecule long-read sequencing has been used to improve mRNA isoform identification. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and sequencing length limits. This drives a ne
Externí odkaz:
https://doaj.org/article/98691d43feca4ef991ee1193f0b0d112
Autor:
Emre Sefer, Carl Kingsford
Publikováno v:
Algorithms for Molecular Biology, Vol 14, Iss 1, Pp 1-11 (2019)
Abstract Background Hi-C experiments capturing the 3D genome architecture have led to the discovery of topologically-associated domains (TADs) that form an important part of the 3D genome organization and appear to play a role in gene regulation and
Externí odkaz:
https://doaj.org/article/7616f78b0ba54f528cd0df67b6af95e6
Publikováno v:
Journal of Computational Biology. 29:1288-1304
Minimizers are widely used to sample representative
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4563c060b1fa528ae0f06e069a4d870c
https://doi.org/10.1089/cmb.2022.0275
https://doi.org/10.1089/cmb.2022.0275