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Volume 36, Issue 22-23, 1 December 2020
REVIEW
SEQUENCE ANALYSIS
Classification and review of free PCR primer design software
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5263–5268, https://doi.org/10.1093/bioinformatics/btaa910
DISCOVERY NOTE
DATA AND TEXT MINING
On biases of attention in scientific discovery
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5269–5274, https://doi.org/10.1093/bioinformatics/btaa1036
ORIGINAL PAPERS
GENOME ANALYSIS
Metagenome SNP calling via read-colored de Bruijn graphs
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5275–5281, https://doi.org/10.1093/bioinformatics/btaa081
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5282–5290, https://doi.org/10.1093/bioinformatics/btaa1015
Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5291–5298, https://doi.org/10.1093/bioinformatics/btaa1044
Issues of Z-factor and an approach to avoid them for quality control in high-throughput screening studies
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5299–5303, https://doi.org/10.1093/bioinformatics/btaa1049
DeepNOG: fast and accurate protein orthologous group assignment
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5304–5312, https://doi.org/10.1093/bioinformatics/btaa1051
SEQUENCE ANALYSIS
Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5313–5321, https://doi.org/10.1093/bioinformatics/btaa1017
DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5322–5329, https://doi.org/10.1093/bioinformatics/btaa1030
SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5330–5336, https://doi.org/10.1093/bioinformatics/btaa1042
Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5337–5343, https://doi.org/10.1093/bioinformatics/btaa1053
Minimally overlapping words for sequence similarity search
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5344–5350, https://doi.org/10.1093/bioinformatics/btaa1054
PHYLOGENETICS
Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5351–5360, https://doi.org/10.1093/bioinformatics/btaa1020
STRUCTURAL BIOINFORMATICS
Improved protein model quality assessment by integrating sequential and pairwise features using deep learning
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5361–5367, https://doi.org/10.1093/bioinformatics/btaa1037
A library of coiled-coil domains: from regular bundles to peculiar twists
Krzysztof Szczepaniak, Adriana Bukala, Antonio Marinho da Silva Neto, Jan Ludwiczak, Stanislaw Dunin-Horkawicz
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5368–5376, https://doi.org/10.1093/bioinformatics/btaa1041
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5377–5385, https://doi.org/10.1093/bioinformatics/btaa1050
GENE EXPRESSION
Autoregressive modeling and diagnostics for qPCR amplification
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5386–5391, https://doi.org/10.1093/bioinformatics/btaa1000
Parallelized calculation of permutation tests
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5392–5397, https://doi.org/10.1093/bioinformatics/btaa1007
New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5398–5404, https://doi.org/10.1093/bioinformatics/btaa1021
Integration of gene interaction information into a reweighted Lasso-Cox model for accurate survival prediction
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5405–5414, https://doi.org/10.1093/bioinformatics/btaa1046
GENETICS AND POPULATION ANALYSIS
A Bayesian linear mixed model for prediction of complex traits
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5415–5423, https://doi.org/10.1093/bioinformatics/btaa1023
LDpred2: better, faster, stronger
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5424–5431, https://doi.org/10.1093/bioinformatics/btaa1029
A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5432–5438, https://doi.org/10.1093/bioinformatics/btaa1055
SYSTEMS BIOLOGY
IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5439–5447, https://doi.org/10.1093/bioinformatics/btaa1001
Prioritizing genes for systematic variant effect mapping
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5448–5455, https://doi.org/10.1093/bioinformatics/btaa1008
Heterogeneous graph inference with matrix completion for computational drug repositioning
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5456–5464, https://doi.org/10.1093/bioinformatics/btaa1024
Complete populations of virtual patients for in silico clinical trials
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5465–5472, https://doi.org/10.1093/bioinformatics/btaa1026
Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5473–5480, https://doi.org/10.1093/bioinformatics/btaa1040
IDDkin: network-based influence deep diffusion model for enhancing prediction of kinase inhibitors
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5481–5491, https://doi.org/10.1093/bioinformatics/btaa1058
DATA AND TEXT MINING
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5492–5498, https://doi.org/10.1093/bioinformatics/btaa1006
PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5499–5506, https://doi.org/10.1093/bioinformatics/btaa1056
DATABASES AND ONTOLOGIES
Virxicon: a lexicon of viral sequences
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5507–5513, https://doi.org/10.1093/bioinformatics/btaa1066
APPLICATIONS NOTES
GENOME ANALYSIS
MOSGA: Modular Open-Source Genome Annotator
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5514–5515, https://doi.org/10.1093/bioinformatics/btaa1003
CAFE 5 models variation in evolutionary rates among gene families
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5516–5518, https://doi.org/10.1093/bioinformatics/btaa1022
SVIM-asm: structural variant detection from haploid and diploid genome assemblies
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5519–5521, https://doi.org/10.1093/bioinformatics/btaa1034
CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5522–5523, https://doi.org/10.1093/bioinformatics/btaa1047
Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5524–5525, https://doi.org/10.1093/bioinformatics/btaa1048
STRUCTURAL BIOINFORMATICS
RCSB Protein Data Bank 1D tools and services
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5526–5527, https://doi.org/10.1093/bioinformatics/btaa1012
MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5528–5529, https://doi.org/10.1093/bioinformatics/btaa1019
crisscrosslinkeR: identification and visualization of protein–RNA and protein–protein interactions from crosslinking mass spectrometry
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5530–5532, https://doi.org/10.1093/bioinformatics/btaa1043
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5533–5534, https://doi.org/10.1093/bioinformatics/btaa1045
GENE EXPRESSION
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5535–5536, https://doi.org/10.1093/bioinformatics/btaa1011
GENETICS AND POPULATION ANALYSIS
Sparse Project VCF: efficient encoding of population genotype matrices
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5537–5538, https://doi.org/10.1093/bioinformatics/btaa1004
SYSTEMS BIOLOGY
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5539–5541, https://doi.org/10.1093/bioinformatics/btaa1018
IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5542–5544, https://doi.org/10.1093/bioinformatics/btaa1025
DATA AND TEXT MINING
DeepPurpose: a deep learning library for drug–target interaction prediction
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5545–5547, https://doi.org/10.1093/bioinformatics/btaa1005
Collecting and managing taxonomic data with NCBI-taxonomist
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5548–5550, https://doi.org/10.1093/bioinformatics/btaa1027
struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5551–5552, https://doi.org/10.1093/bioinformatics/btaa1031
PETAL: a Python tool for deep analysis of biological pathways
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5553–5555, https://doi.org/10.1093/bioinformatics/btaa1032
aCLImatise: automated generation of tool definitions for bioinformatics workflows
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5556–5557, https://doi.org/10.1093/bioinformatics/btaa1033
LETTER TO THE EDITOR
GENOME ANALYSIS
Comment on ‘Hayai-Annotation Plants: an ultrafast and comprehensive functional gene annotation system in plants’: the importance of taking the GO graph structure into account
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5558–5560, https://doi.org/10.1093/bioinformatics/btaa1052
CORRIGENDA
Corrigendum to: HALPER facilitates the identification of regulatory element orthologs across species
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Page 5561, https://doi.org/10.1093/bioinformatics/btaa1013
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Page 5562, https://doi.org/10.1093/bioinformatics/btaa663
CMF-Impute: an accurate imputation tool for single cell RNA-seq data
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5563–5564, https://doi.org/10.1093/bioinformatics/btaa664
LBERT: Lexically-aware Transformers based Bidirectional Encoder Representation model for learning Universal Bio-Entity Relations
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Page 5565, https://doi.org/10.1093/bioinformatics/btaa869
ERRATUM
LFQC: A lossless compression algorithm for FASTQ files
Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Page 5566, https://doi.org/10.1093/bioinformatics/btaa1035
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