Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Anish M. S. Shrestha"'
Publikováno v:
BMC Bioinformatics, Vol 25, Iss S2, Pp 1-15 (2024)
Abstract Background Conventional differential gene expression analysis pipelines for non-model organisms require computationally expensive transcriptome assembly. We recently proposed an alternative strategy of directly aligning RNA-seq reads to a pr
Externí odkaz:
https://doaj.org/article/be4eff8e04bf4b17b00e898db06e75f0
Publikováno v:
Bioinformatics
Motivation Split-alignments provide base-pair-resolution evidence of genomic rearrangements. In practice, they are found by first computing high-scoring local alignments, parts of which are then combined into a split-alignment. This approach is chall
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f430b8060bc8b064eac96219e3e9286f
https://doi.org/10.1093/bioinformatics/bty398
https://doi.org/10.1093/bioinformatics/bty398
Autor:
Anish M S Shrestha, Martin C. Frith
Publikováno v:
IEEE/ACM transactions on computational biology and bioinformatics. 15(6)
Finding related nucleotide or protein sequences is a fundamental, diverse, and incompletely-solved problem in bioinformatics. It is often tackled by seed-and-extend methods, which first find “seed” matches of diverse types, such as spaced seeds,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b0a9e92e021f7f2208a938c5c67d147d
https://pubmed.ncbi.nlm.nih.gov/29994365
https://pubmed.ncbi.nlm.nih.gov/29994365
Autor:
Martin C. Frith, Anish M S Shrestha
Publikováno v:
Bioinformatics
Summary: Many high-throughput sequencing experiments produce paired DNA reads. Paired-end DNA reads provide extra positional information that is useful in reliable mapping of short reads to a reference genome, as well as in downstream analyses of str
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bdbe265a37bd65a2c2cf67359d9a40ff
https://doi.org/10.1093/bioinformatics/btt073
https://doi.org/10.1093/bioinformatics/btt073
Autor:
Santiago, Kyle Christian L.1,2 (AUTHOR), Shrestha, Anish M. S.1,2 (AUTHOR) anish.shrestha@dlsu.edu.ph
Publikováno v:
BMC Bioinformatics. 10/24/2024, Vol. 25 Issue 1, p1-14. 14p.
Publikováno v:
Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2018, 46 (3), pp.e18. ⟨10.1093/nar/gkx1175⟩
Nucleic Acids Research, Oxford University Press, 2018, 46 (3), pp.e18. ⟨10.1093/nar/gkx1175⟩
International audience; Performing sequence alignment to identify structural variants, such as large deletions, from genome se-quencing data is a fundamental task, but current methods are far from perfect. The current practice is to independently ali
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b68edcfe180d9c6f9348df40cf63a4cc
http://europepmc.org/articles/PMC5815140
http://europepmc.org/articles/PMC5815140
Publikováno v:
Briefings in Bioinformatics
The suffix array and its variants are text-indexing data structures that have become indispensable in the field of bioinformatics. With the uninitiated in mind, we provide an accessible exposition of the SA-IS algorithm, which is the state of the art
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::54f142ed2273292f35e774035994a097
https://pubmed.ncbi.nlm.nih.gov/24413184
https://pubmed.ncbi.nlm.nih.gov/24413184
Autor:
Gonzales, Mark Edward M.1,2 (AUTHOR), Ureta, Jennifer C.1,2 (AUTHOR), Shrestha, Anish M. S.1,2,3 (AUTHOR) anish.shrestha@dlsu.edu.ph
Publikováno v:
PLoS ONE. 7/24/2023, Vol. 18 Issue 7, p1-22. 22p.
Publikováno v:
IEEE/ACM Transactions on Computational Biology & Bioinformatics; Nov/Dec2018, Vol. 15 Issue 6, p2067-2073, 7p
Combining probabilistic alignments with read pair information improves accuracy of split-alignments.
Publikováno v:
Bioinformatics; Nov2018, Vol. 34 Issue 21, p3631-3637, 7p