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Volume 34, Issue 21, November 2018
ORIGINAL PAPERS
GENOME ANALYSIS
Indexed variation graphs for efficient and accurate resistome profiling
Will P M Rowe and Martyn D Winn
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3601–3608, https://doi.org/10.1093/bioinformatics/bty387
Pathway-structured predictive modeling for multi-level drug response in multiple myeloma
Xinyan Zhang and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3609–3615, https://doi.org/10.1093/bioinformatics/bty436
SEQUENCE ANALYSIS
Predicting gene structure changes resulting from genetic variants via exon definition features
William H Majoros and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3616–3623, https://doi.org/10.1093/bioinformatics/bty324
Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA)
Le Zhang and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3624–3630, https://doi.org/10.1093/bioinformatics/bty392
Combining probabilistic alignments with read pair information improves accuracy of split-alignments
Anish M S Shrestha and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3631–3637, https://doi.org/10.1093/bioinformatics/bty398
PHYLOGENETICS
Exact Bayesian inference for phylogenetic birth-death models
Kris V Parag and Oliver G Pybus
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3638–3645, https://doi.org/10.1093/bioinformatics/bty337
RecPhyloXML: a format for reconciled gene trees
Wandrille Duchemin and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3646–3652, https://doi.org/10.1093/bioinformatics/bty389
STRUCTURAL BIOINFORMATICS
Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation
Dinara R Usmanova and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3653–3658, https://doi.org/10.1093/bioinformatics/bty340
Quantification of biases in predictions of protein stability changes upon mutations
Fabrizio Pucci and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3659–3665, https://doi.org/10.1093/bioinformatics/bty348
Development and evaluation of a deep learning model for protein–ligand binding affinity prediction
Marta M Stepniewska-Dziubinska and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3666–3674, https://doi.org/10.1093/bioinformatics/bty374
Bio-knowledge-based filters improve residue–residue contact prediction accuracy
P P Wozniak and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3675–3683, https://doi.org/10.1093/bioinformatics/bty416
GENE EXPRESSION
Single cell clustering based on cell-pair differentiability correlation and variance analysis
Hao Jiang and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3684–3694, https://doi.org/10.1093/bioinformatics/bty390
GENETICS AND POPULATION ANALYSIS
Detection of multi-dimensional co-exclusion patterns in microbial communities
Levent Albayrak and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3695–3701, https://doi.org/10.1093/bioinformatics/bty414
SYSTEMS BIOLOGY
PyCoTools: a Python toolbox for COPASI
Ciaran M Welsh and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3702–3710, https://doi.org/10.1093/bioinformatics/bty409
DATA AND TEXT MINING
The revival of the Gini importance?
Stefano Nembrini and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3711–3718, https://doi.org/10.1093/bioinformatics/bty373
EBIC: an evolutionary-based parallel biclustering algorithm for pattern discovery
Patryk Orzechowski and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3719–3726, https://doi.org/10.1093/bioinformatics/bty401
A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data
Yunchuan Kong and Tianwei Yu
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3727–3737, https://doi.org/10.1093/bioinformatics/bty429
APPLICATIONS NOTES
GENOME ANALYSIS
ConSpeciFix: classifying prokaryotic species based on gene flow
Louis-Marie Bobay and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3738–3740, https://doi.org/10.1093/bioinformatics/bty400
mEBT: multiple-matching evidence-based translator of murine genomic responses for human immunity studies
Donghyun Tae and Junhee Seok
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3741–3743, https://doi.org/10.1093/bioinformatics/bty431
SEQUENCE ANALYSIS
AC-DIAMOND v1: accelerating large-scale DNA–protein alignment
Huijun Mai and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3744–3746, https://doi.org/10.1093/bioinformatics/bty391
PEA: an integrated R toolkit for plant epitranscriptome analysis
Jingjing Zhai and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3747–3749, https://doi.org/10.1093/bioinformatics/bty421
LiveKraken––real-time metagenomic classification of illumina data
Simon H Tausch and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3750–3752, https://doi.org/10.1093/bioinformatics/bty433
MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database
Matthieu Leray and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3753–3754, https://doi.org/10.1093/bioinformatics/bty454
STRUCTURAL BIOINFORMATICS
NGL viewer: web-based molecular graphics for large complexes
Alexander S Rose and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3755–3758, https://doi.org/10.1093/bioinformatics/bty419
MODE-TASK: large-scale protein motion tools
Caroline Ross and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3759–3763, https://doi.org/10.1093/bioinformatics/bty427
SYSTEMS BIOLOGY
TimeXNet Web: identifying cellular response networks from diverse omics time-course data
Phit Ling Tan and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3764–3765, https://doi.org/10.1093/bioinformatics/bty393
Using meshes for MeSH term enrichment and semantic analyses
Guangchuang Yu
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3766–3767, https://doi.org/10.1093/bioinformatics/bty410
DATABASES AND ONTOLOGIES
SoS Notebook: an interactive multi-language data analysis environment
Bo Peng and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3768–3770, https://doi.org/10.1093/bioinformatics/bty405
GSCALite: a web server for gene set cancer analysis
Chun-Jie Liu and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3771–3772, https://doi.org/10.1093/bioinformatics/bty411
Exploring drug space with ChemMaps.com
Alexandre Borrel and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3773–3775, https://doi.org/10.1093/bioinformatics/bty412
BIOIMAGE INFORMATICS
TomoEED: fast edge-enhancing denoising of tomographic volumes
J J Moreno and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3776–3778, https://doi.org/10.1093/bioinformatics/bty435
CORRIGENDA
DDR: efficient computational method to predict drug–target interactions using graph mining and machine learning approaches
Rawan S Olayan and others
Bioinformatics, Volume 34, Issue 21, November 2018, Page 3779, https://doi.org/10.1093/bioinformatics/bty417
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework
Nikolaos Tsiantis and others
Bioinformatics, Volume 34, Issue 21, November 2018, Page 3780, https://doi.org/10.1093/bioinformatics/bty438
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