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Volume 35, Issue 2, January 2019
ORIGINAL PAPERS
GENOME ANALYSIS
Using tree-based methods for detection of gene–gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 181–188, https://doi.org/10.1093/bioinformatics/bty462
ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 189–199, https://doi.org/10.1093/bioinformatics/bty511
Statistical tests for detecting variance effects in quantitative trait studies
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 200–210, https://doi.org/10.1093/bioinformatics/bty565
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 211–218, https://doi.org/10.1093/bioinformatics/bty592
Metagenomic binning through low-density hashing
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 219–226, https://doi.org/10.1093/bioinformatics/bty611
SEQUENCE ANALYSIS
CoMSA: compression of protein multiple sequence alignment files
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 227–234, https://doi.org/10.1093/bioinformatics/bty619
STRUCTURAL BIOINFORMATICS
Computational analysis of kinase inhibitor selectivity using structural knowledge
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 235–242, https://doi.org/10.1093/bioinformatics/bty582
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 243–250, https://doi.org/10.1093/bioinformatics/bty583
GENE EXPRESSION
Xolik: finding cross-linked peptides with maximum paired scores in linear time
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 251–257, https://doi.org/10.1093/bioinformatics/bty526
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 258–265, https://doi.org/10.1093/bioinformatics/bty629
SYSTEMS BIOLOGY
Flux tope analysis: studying the coordination of reaction directions in metabolic networks
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 266–273, https://doi.org/10.1093/bioinformatics/bty550
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 274–283, https://doi.org/10.1093/bioinformatics/bty577
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 284–292, https://doi.org/10.1093/bioinformatics/bty607
DATA AND TEXT MINING
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 293–300, https://doi.org/10.1093/bioinformatics/bty465
Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 301–308, https://doi.org/10.1093/bioinformatics/bty491
Compound–protein interaction prediction with end-to-end learning of neural networks for graphs and sequences
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 309–318, https://doi.org/10.1093/bioinformatics/bty535
BIOIMAGE INFORMATICS
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 319–328, https://doi.org/10.1093/bioinformatics/bty620
APPLICATIONS NOTES
GENOME ANALYSIS
GeneSpy, a user-friendly and flexible genomic context visualizer
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 329–331, https://doi.org/10.1093/bioinformatics/bty459
SEQUENCE ANALYSIS
3DPatch: fast 3D structure visualization with residue conservation
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 332–334, https://doi.org/10.1093/bioinformatics/bty464
PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 335–336, https://doi.org/10.1093/bioinformatics/bty578
Crumble: reference free lossy compression of sequence quality values
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 337–339, https://doi.org/10.1093/bioinformatics/bty608
GENE EXPRESSION
TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 340–342, https://doi.org/10.1093/bioinformatics/bty483
BrainImageR: spatiotemporal gene set analysis referencing the human brain
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 343–345, https://doi.org/10.1093/bioinformatics/bty618
SYSTEMS BIOLOGY
SLIDE – a web-based tool for interactive visualization of large-scale – omics data
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 346–348, https://doi.org/10.1093/bioinformatics/bty534
DATABASES AND ONTOLOGIES
SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 349–351, https://doi.org/10.1093/bioinformatics/bty549
REVIEW
DATABASES AND ONTOLOGIES
Exosomal lncRNAs and cancer: connecting the missing links
Bioinformatics, Volume 35, Issue 2, January 2019, Pages 352–360, https://doi.org/10.1093/bioinformatics/bty527
