Suppr超能文献

A Python-based programming language for high-performance computational genomics.

作者信息

Shajii Ariya, Numanagić Ibrahim, Leighton Alexander T, Greenyer Haley, Amarasinghe Saman, Berger Bonnie

机构信息

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.

Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada.

出版信息

Nat Biotechnol. 2021 Sep;39(9):1062-1064. doi: 10.1038/s41587-021-00985-6.

Abstract
摘要

相似文献

1
A Python-based programming language for high-performance computational genomics.
Nat Biotechnol. 2021 Sep;39(9):1062-1064. doi: 10.1038/s41587-021-00985-6.
2
The Essential Toolbox of Data Science: Python, R, Git, and Docker.
Methods Mol Biol. 2020;2104:265-311. doi: 10.1007/978-1-0716-0239-3_15.
3
A comparison of common programming languages used in bioinformatics.
BMC Bioinformatics. 2008 Feb 5;9:82. doi: 10.1186/1471-2105-9-82.
4
An Introduction to Programming for Bioscientists: A Python-Based Primer.
PLoS Comput Biol. 2016 Jun 7;12(6):e1004867. doi: 10.1371/journal.pcbi.1004867. eCollection 2016 Jun.
5
A quick guide to teaching R programming to computational biology students.
PLoS Comput Biol. 2009 Aug;5(8):e1000482. doi: 10.1371/journal.pcbi.1000482. Epub 2009 Aug 28.
6
The Ensembl REST API: Ensembl Data for Any Language.
Bioinformatics. 2015 Jan 1;31(1):143-5. doi: 10.1093/bioinformatics/btu613. Epub 2014 Sep 17.
7
SciPy 1.0: fundamental algorithms for scientific computing in Python.
Nat Methods. 2020 Mar;17(3):261-272. doi: 10.1038/s41592-019-0686-2. Epub 2020 Feb 3.
8
Bench pressing with genomics benchmarkers.
Nat Methods. 2020 Mar;17(3):255-258. doi: 10.1038/s41592-020-0768-1.
9
hts-nim: scripting high-performance genomic analyses.
Bioinformatics. 2018 Oct 1;34(19):3387-3389. doi: 10.1093/bioinformatics/bty358.
10
Programming languages for circuit design.
Methods Mol Biol. 2015;1244:81-104. doi: 10.1007/978-1-4939-1878-2_5.

引用本文的文献

1
Pytrf: a python package for finding tandem repeats from genomic sequences.
BMC Bioinformatics. 2025 Jun 4;26(1):151. doi: 10.1186/s12859-025-06168-3.
2
Efficient mapping of accurate long reads in minimizer space with mapquik.
Genome Res. 2023 Jul;33(7):1188-1197. doi: 10.1101/gr.277679.123. Epub 2023 Jun 30.
4
Navigating bottlenecks and trade-offs in genomic data analysis.
Nat Rev Genet. 2023 Apr;24(4):235-250. doi: 10.1038/s41576-022-00551-z. Epub 2022 Dec 7.
5
Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines.
IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2022 May-Jun;2022:164-165. Epub 2022 Aug 1.
6
Fast characterization of segmental duplication structure in multiple genome assemblies.
Algorithms Mol Biol. 2022 Mar 18;17(1):4. doi: 10.1186/s13015-022-00210-2.
7
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.
Cell Syst. 2021 Oct 20;12(10):958-968.e6. doi: 10.1016/j.cels.2021.08.009. Epub 2021 Sep 14.

本文引用的文献

1
Seq: A High-Performance Language for Bioinformatics.
Proc ACM Program Lang. 2019 Oct;3. doi: 10.1145/3360551. Epub 2019 Oct 10.
2
Why scientists are turning to Rust.
Nature. 2020 Dec;588(7836):185-186. doi: 10.1038/d41586-020-03382-2.
4
Reproducibility in science: important or incremental?
Lancet Microbe. 2020 Jun;1(2):e59-60. doi: 10.1016/S2666-5247(20)30028-8. Epub 2020 May 14.
5
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191.
6
The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.
J Biotechnol. 2017 Nov 10;261:157-168. doi: 10.1016/j.jbiotec.2017.07.017. Epub 2017 Sep 6.
7
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.
Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18.
8
1,500 scientists lift the lid on reproducibility.
Nature. 2016 May 26;533(7604):452-4. doi: 10.1038/533452a.
9
Compressive mapping for next-generation sequencing.
Nat Biotechnol. 2016 Apr;34(4):374-6. doi: 10.1038/nbt.3511.
10
Rust-Bio: a fast and safe bioinformatics library.
Bioinformatics. 2016 Feb 1;32(3):444-6. doi: 10.1093/bioinformatics/btv573. Epub 2015 Oct 6.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验