Zobrazeno 1 - 10
of 93
pro vyhledávání: '"Rob Patro"'
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-16 (2024)
Abstract Purpose String indexes such as the suffix array (sa) and the closely related longest common prefix (lcp) array are fundamental objects in bioinformatics and have a wide variety of applications. Despite their importance in practice, few scala
Externí odkaz:
https://doaj.org/article/79aae57e7f2345199d9e1c1cff770744
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-21 (2024)
Abstract The problem of sequence identification or matching—determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence—is relevant for many important tasks in Computationa
Externí odkaz:
https://doaj.org/article/edf66e1b8cdf44abb9a00887e9b5d8c5
Autor:
Euphy Y. Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro, Michael I. Love
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-21 (2023)
Abstract Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution,
Externí odkaz:
https://doaj.org/article/9853abdefa264d67a0c9007ce9680240
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-32 (2022)
Abstract The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computationa
Externí odkaz:
https://doaj.org/article/2703e9a921a44a128101d491a0a0481e
Publikováno v:
iScience, Vol 26, Iss 6, Pp 106961- (2023)
Summary: A certain degree of uncertainty is always associated with the transcript abundance estimates. The uncertainty may make many downstream analyses, such as differential testing, difficult for certain transcripts. Conversely, gene-level analysis
Externí odkaz:
https://doaj.org/article/97ec224d99d64b6aaed3e54e6ba229b8
Publikováno v:
Algorithms for Molecular Biology, Vol 17, Iss 1, Pp 1-23 (2022)
Abstract Background There has been rapid development of probabilistic models and inference methods for transcript abundance estimation from RNA-seq data. These models aim to accurately estimate transcript-level abundances, to account for different bi
Externí odkaz:
https://doaj.org/article/ddc5bc806d2d448f8708516c9cf8face
Autor:
Giorgos Skoufos, Fatemeh Almodaresi, Mohsen Zakeri, Joseph N. Paulson, Rob Patro, Artemis G. Hatzigeorgiou, Ioannis S. Vlachos
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-27 (2022)
Abstract We introduce AGAMEMNON ( https://github.com/ivlachos/agamemnon ) for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples, single-microbe sequencing experiments, or sequenced host samples. AGAMEMNO
Externí odkaz:
https://doaj.org/article/8865be1ef2df4992946f1cc082efc81d
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:
Genome Biology, Vol 20, Iss 1, Pp 1-16 (2019)
Abstract We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barco
Externí odkaz:
https://doaj.org/article/0fd3e361ed254020a5219a3e4163d9e4
Autor:
Rob Patro, Leena Salmela
Publikováno v:
iScience, Vol 24, Iss 1, Pp 101956- (2021)
Summary: DNA and RNA sequencing is a core technology in biological and medical research. The high throughput of these technologies and the consistent development of new experimental assays and biotechnologies demand the continuous development of meth
Externí odkaz:
https://doaj.org/article/6b821be5a7a841a2a0f3ef97180e88b9