Zobrazeno 1 - 10
of 42
pro vyhledávání: '"Mingfu Shao"'
Autor:
Ke Chen, Mingfu Shao
Publikováno v:
Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-13 (2023)
Abstract Background Many bioinformatics applications involve bucketing a set of sequences where each sequence is allowed to be assigned into multiple buckets. To achieve both high sensitivity and precision, bucketing methods are desired to assign sim
Externí odkaz:
https://doaj.org/article/d94414ea00ea4731860621927db839ab
Autor:
Qimin Zhang, Mingfu Shao
Publikováno v:
PLoS Computational Biology, Vol 19, Iss 12, p e1011734 (2023)
Transcript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their methodo
Externí odkaz:
https://doaj.org/article/9affb20fcd454252a08f86d85045e38f
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
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
Publikováno v:
Genome Biology, Vol 19, Iss 1, Pp 1-16 (2018)
Abstract Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting these modifications, called transc
Externí odkaz:
https://doaj.org/article/aded1431394348bb8ee4fcb35037a556
Publikováno v:
Nat Comput Sci
Modern RNA-sequencing protocols can produce multi-end data, where multiple reads originating from the same transcript are attached to the same barcode. The long-range information in the multi-end reads is beneficial in phasing complicated spliced iso
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7e73c9d81be95c82567b26fe632a9180
https://doi.org/10.1038/s43588-022-00216-1
https://doi.org/10.1038/s43588-022-00216-1
Transcript assembly (i.e., to reconstruct the full-length expressed transcripts from RNA-seq data) has been a critical but yet unsolved step in RNA-seq analysis. Modern RNA-seq protocols can produce paired-/multiple-end RNA-seq reads, where informati
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::29c90a33265ca1956ab26dd305052169
https://doi.org/10.1101/2021.09.03.458862
https://doi.org/10.1101/2021.09.03.458862
MotivationThe widely-used high-throughput RNA-sequencing technologies (RNA-seq) usually produce paired-end reads. We explore if full fragments can be computationally reconstructed from the sequenced two ends—a problem here we refer to as bridging.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7eb76884c6283ae780803896b55f853f
https://doi.org/10.1101/2021.02.26.433113
https://doi.org/10.1101/2021.02.26.433113
Autor:
Qian Shi, Mingfu Shao
MotivationThe established high-throughput RNA-seq technologies usually produce paired-end reads. A challenging problem is therefore to computationally infer the alignment of entire fragments given the alignment of the two mate ends. Solving this prob
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d7909b49f9554db95e2135376ce1aa31
https://doi.org/10.1101/2020.03.03.975821
https://doi.org/10.1101/2020.03.03.975821
Autor:
Bernard M. E. Moret, Mingfu Shao
Publikováno v:
Lecture Notes in Computer Science ISBN: 9783319319568
RECOMB
RECOMB
A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or syntenic blocks). For two genomes without duplicate genes, we can easily define (and almost alwa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79ad36806baa177430450ab08a24e251
https://doi.org/10.1089/cmb.2016.0149
https://doi.org/10.1089/cmb.2016.0149