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Volume 3, Issue 1, March 2021
High Throughput Sequencing Methods
Increased yields of duplex sequencing data by a series of quality control tools
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab002, https://doi.org/10.1093/nargab/lqab002
Articles
CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa107, https://doi.org/10.1093/nargab/lqaa107
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa108, https://doi.org/10.1093/nargab/lqaa108
Rapid discovery of novel prophages using biological feature engineering and machine learning
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa109, https://doi.org/10.1093/nargab/lqaa109
A new graph-based clustering method with application to single-cell RNA-seq data from human pancreatic islets
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa087, https://doi.org/10.1093/nargab/lqaa087
PanACoTA: a modular tool for massive microbial comparative genomics
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa106, https://doi.org/10.1093/nargab/lqaa106
Computational deconvolution to estimate cell type-specific gene expression from bulk data
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa110, https://doi.org/10.1093/nargab/lqaa110
Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense–antisense pairs
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa111, https://doi.org/10.1093/nargab/lqaa111
The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa113, https://doi.org/10.1093/nargab/lqaa113
In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa112, https://doi.org/10.1093/nargab/lqaa112
Identity: rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab001, https://doi.org/10.1093/nargab/lqab001
ClipSV: improving structural variation detection by read extension, spliced alignment and tree-based decision rules
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab003, https://doi.org/10.1093/nargab/lqab003
Interpretable detection of novel human viruses from genome sequencing data
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab004, https://doi.org/10.1093/nargab/lqab004
Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab007, https://doi.org/10.1093/nargab/lqab007
A comparative study of protein–ssDNA interactions
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab006, https://doi.org/10.1093/nargab/lqab006
TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab008, https://doi.org/10.1093/nargab/lqab008
Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab011, https://doi.org/10.1093/nargab/lqab011
F-Seq2: improving the feature density based peak caller with dynamic statistics
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab012, https://doi.org/10.1093/nargab/lqab012
CRISPR-SE: a brute force search engine for CRISPR design
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab013, https://doi.org/10.1093/nargab/lqab013
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab010, https://doi.org/10.1093/nargab/lqab010
Increased yields of duplex sequencing data by a series of quality control tools
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab014, https://doi.org/10.1093/nargab/lqab014
3D reconstruction of genomic regions from sparse interaction data
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab017, https://doi.org/10.1093/nargab/lqab017
ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab018, https://doi.org/10.1093/nargab/lqab018
Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab021, https://doi.org/10.1093/nargab/lqab021
Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab020, https://doi.org/10.1093/nargab/lqab020
Methods Article
Probabilistic outlier identification for RNA sequencing generalized linear models
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab005, https://doi.org/10.1093/nargab/lqab005
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab009, https://doi.org/10.1093/nargab/lqab009
Two-stage Cox-nnet: biologically interpretable neural-network model for prognosis prediction and its application in liver cancer survival using histopathology and transcriptomic data
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab015, https://doi.org/10.1093/nargab/lqab015
Sequencing error profiles of Illumina sequencing instruments
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqab019, https://doi.org/10.1093/nargab/lqab019
