Zobrazeno 1 - 10
of 35
pro vyhledávání: '"Kristoffer Sahlin"'
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-23 (2023)
Abstract It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to a
Externí odkaz:
https://doaj.org/article/f296d9beff9147898bdc9aaddd7aa3fd
Autor:
Alice Namias, Kristoffer Sahlin, Patrick Makoundou, Iago Bonnici, Mathieu Sicard, Khalid Belkhir, Mylène Weill
Publikováno v:
Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 3656-3664 (2023)
The importance of gene amplifications in evolution is more and more recognized. Yet, tools to study multi-copy gene families are still scarce, and many such families are overlooked using common sequencing methods. Haplotype reconstruction is even har
Externí odkaz:
https://doaj.org/article/7c24373d59bb4b0fa6fb39009d77cf5e
Autor:
Kristoffer Sahlin
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-27 (2022)
Abstract Read alignment is often the computational bottleneck in analyses. Recently, several advances have been made on seeding methods for fast sequence comparison. We combine two such methods, syncmers and strobemers, in a novel seeding approach fo
Externí odkaz:
https://doaj.org/article/0cee7d1b8fad4cf5ac2ffd833ef576f3
Publikováno v:
Ecology and Evolution, Vol 11, Iss 3, Pp 1392-1398 (2021)
Abstract Third‐generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long‐read sequences. This is not
Externí odkaz:
https://doaj.org/article/40fddca195964d17bc4d5f95ff639f37
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-13 (2021)
Nanopore sequencing technologies applied to transcriptome analysis suffer from high error rates, limiting them largely to reference-based analyses. Here, the authors develop a computational error correction method for transcriptome analysis that redu
Externí odkaz:
https://doaj.org/article/c58996ac31174cc1880dbd2c6ce0a3a8
Autor:
Samarth Rangavittal, Natasha Stopa, Marta Tomaszkiewicz, Kristoffer Sahlin, Kateryna D. Makova, Paul Medvedev
Publikováno v:
BMC Genomics, Vol 20, Iss 1, Pp 1-11 (2019)
Abstract Background Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly b
Externí odkaz:
https://doaj.org/article/854294d6ad0240a4be26eba88f63087a
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-12 (2018)
Transcripts from highly-similar multigene families are challenging to decipher. Here, the authors develop IsoCon, a tool for detecting and reconstructing isoforms from multigene families by analyzing long PacBio Iso-Seq reads.
Externí odkaz:
https://doaj.org/article/9f5d8d47200944ad99df5bbd232614b8
Autor:
Kristoffer Sahlin, Paul Medvedev
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-1 (2021)
A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21424-9
Externí odkaz:
https://doaj.org/article/33a7513450c64bff89d589e6de2809ac
Publikováno v:
bioRxiv
Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been recently studied in great ape
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a5fbab6a8edb90c42d89d6d867ebb1f1
https://europepmc.org/articles/PMC10054944/
https://europepmc.org/articles/PMC10054944/
DNA sequencing data continues to progress towards longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (PacBio HiFi) to a reference genome, whi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8d193e1b9cc261939b1505244be7b56a
https://doi.org/10.1101/2022.12.23.521809
https://doi.org/10.1101/2022.12.23.521809