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Volume 37, Issue 24, December 2021
REVIEW
SEQUENCE ANALYSIS
iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization
Yingying Yu and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4603–4610, https://doi.org/10.1093/bioinformatics/btab677
ORIGINAL PAPERS
GENOME ANALYSIS
Founder reconstruction enables scalable and seamless pangenomic analysis
Tuukka Norri and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4611–4619, https://doi.org/10.1093/bioinformatics/btab516
Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data
Niko Popitsch and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4620–4625, https://doi.org/10.1093/bioinformatics/btab526
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints
Dhong-Gun Won and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4626–4634, https://doi.org/10.1093/bioinformatics/btab529
CCIP: predicting CTCF-mediated chromatin loops with transitivity
Weibing Wang and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4635–4642, https://doi.org/10.1093/bioinformatics/btab534
Accurate spliced alignment of long RNA sequencing reads
Kristoffer Sahlin and Veli Mäkinen
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4643–4651, https://doi.org/10.1093/bioinformatics/btab540
Transformation and differential abundance analysis of microbiome data incorporating phylogeny
Chao Zhou and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4652–4660, https://doi.org/10.1093/bioinformatics/btab543
Nanopore base calling on the edge
Peter Perešíni and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4661–4667, https://doi.org/10.1093/bioinformatics/btab528
SEQUENCE ANALYSIS
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information
Hangyuan Yang and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4668–4676, https://doi.org/10.1093/bioinformatics/btab551
Accurate large-scale phylogeny-aware alignment using BAli-Phy
Maya Gupta and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4677–4683, https://doi.org/10.1093/bioinformatics/btab555
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides
Wenjia He and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4684–4693, https://doi.org/10.1093/bioinformatics/btab560
An astonishing wealth of new proteasome homologs
Adrian C D Fuchs and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4694–4703, https://doi.org/10.1093/bioinformatics/btab558
PHYLOGENETICS
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data
Haoyun Lei and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4704–4711, https://doi.org/10.1093/bioinformatics/btab504
STRUCTURAL BIOINFORMATICS
Phosphate binding sites prediction in phosphorylation-dependent protein–protein interactions
Zheng-Chang Lu and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4712–4718, https://doi.org/10.1093/bioinformatics/btab525
GENE EXPRESSION
Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)
Akila J Seneviratne and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4719–4726, https://doi.org/10.1093/bioinformatics/btab563
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells
Yixin Zhao and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4727–4736, https://doi.org/10.1093/bioinformatics/btab582
GENETICS AND POPULATION ANALYSIS
Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants
Shuang Song and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4737–4743, https://doi.org/10.1093/bioinformatics/btab514
LINADMIX: evaluating the effect of ancient admixture events on modern populations
Lily Agranat-Tamir and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4744–4755, https://doi.org/10.1093/bioinformatics/btab531
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl
Benjamin B Chu and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4756–4763, https://doi.org/10.1093/bioinformatics/btab489
CHIT: an allele-specific method for testing the association between molecular quantitative traits and phenotype–genotype interaction
Qi Yan and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4764–4770, https://doi.org/10.1093/bioinformatics/btab554
SYSTEMS BIOLOGY
Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction
Xiaodi Yang and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4771–4778, https://doi.org/10.1093/bioinformatics/btab533
Cancer subtype identification by consensus guided graph autoencoders
Cheng Liang and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4779–4786, https://doi.org/10.1093/bioinformatics/btab535
GdClean: removal of Gadolinium contamination in mass cytometry data
Junwei Liu and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4787–4792, https://doi.org/10.1093/bioinformatics/btab537
BioERP: biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions
Xiaoqi Wang and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4793–4800, https://doi.org/10.1093/bioinformatics/btab565
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets
D A Salazar and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4801–4809, https://doi.org/10.1093/bioinformatics/btab579
DATA AND TEXT MINING
Stable Iterative Variable Selection
Mehrad Mahmoudian and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4810–4817, https://doi.org/10.1093/bioinformatics/btab501
DMIL-IsoFun: predicting isoform function using deep multi-instance learning
Guoxian Yu and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4818–4825, https://doi.org/10.1093/bioinformatics/btab532
Organism-specific training improves performance of linear B-cell epitope prediction
Jodie Ashford and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4826–4834, https://doi.org/10.1093/bioinformatics/btab536
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions
Tilman Hinnerichs and Robert Hoehndorf
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4835–4843, https://doi.org/10.1093/bioinformatics/btab548
BIOIMAGE INFORMATICS
Automatic improvement of deep learning-based cell segmentation in time-lapse microscopy by neural architecture search
Yanming Zhu and Erik Meijering
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4844–4850, https://doi.org/10.1093/bioinformatics/btab556
spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos
Wim Thiels and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4851–4856, https://doi.org/10.1093/bioinformatics/btab557
APPLICATIONS NOTES
GENOME ANALYSIS
Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data
Parker Knight and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4857–4859, https://doi.org/10.1093/bioinformatics/btab438
Unfazed: parent-of-origin detection for large and small de novo variants
Jonathan R Belyeu and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4860–4861, https://doi.org/10.1093/bioinformatics/btab454
SEQUENCE ANALYSIS
RENANO: a REference-based compressor for NANOpore FASTQ files
Guillermo Dufort y Álvarez and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4862–4864, https://doi.org/10.1093/bioinformatics/btab437
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity
Sebastiaan Valkiers and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4865–4867, https://doi.org/10.1093/bioinformatics/btab446
PHYLOGENETICS
SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction
Andreas Rempel and Roland Wittler
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4868–4870, https://doi.org/10.1093/bioinformatics/btab444
STRUCTURAL BIOINFORMATICS
Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data
Hamed Khakzad and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4871–4872, https://doi.org/10.1093/bioinformatics/btab449
VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures
Kliment Olechnovič and Česlovas Venclovas
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4873–4875, https://doi.org/10.1093/bioinformatics/btab448
NaViA: a program for the visual analysis of complex mass spectra
Daniel Quetschlich and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4876–4878, https://doi.org/10.1093/bioinformatics/btab436
GENE EXPRESSION
AQUARIUM: accurate quantification of circular isoforms using model-based strategy
Guoxia Wen and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4879–4881, https://doi.org/10.1093/bioinformatics/btab435
GENETICS AND POPULATION ANALYSIS
fastsimcoal2: demographic inference under complex evolutionary scenarios
Laurent Excoffier and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4882–4885, https://doi.org/10.1093/bioinformatics/btab468
SYSTEMS BIOLOGY
peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC–MS profiling datasets
Arnaud M Wolfer and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4886–4888, https://doi.org/10.1093/bioinformatics/btab433
PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX
François Moreews and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4889–4891, https://doi.org/10.1093/bioinformatics/btab441
DATA AND TEXT MINING
The DNA methylation haplotype (mHap) format and mHapTools
Zhiqiang Zhang and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4892–4894, https://doi.org/10.1093/bioinformatics/btab458
DUI: the drug use insights web server
Zachary Prince and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4895–4897, https://doi.org/10.1093/bioinformatics/btab461
DATABASES AND ONTOLOGIES
libOmexMeta: enabling semantic annotation of models to support FAIR principles
Ciaran Welsh and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4898–4900, https://doi.org/10.1093/bioinformatics/btab445
BIOIMAGE INFORMATICS
3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax
Benjamin Schmid and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4901–4902, https://doi.org/10.1093/bioinformatics/btab462
CORRIGENDUM
Corrigendum to: LipidQuant 1.0: automated data processing in lipid class separation–mass spectrometry quantitative workflows
Denise Wolrab and others
Bioinformatics, Volume 37, Issue 24, December 2021, Page 4903, https://doi.org/10.1093/bioinformatics/btab707
ERRATUM
Erratum to: BAli-Phy version 3: model-based co-estimation of alignment and phylogeny
Benjamin D Redelings
Bioinformatics, Volume 37, Issue 24, December 2021, Page 4904, https://doi.org/10.1093/bioinformatics/btab734
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