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Volume 35, Issue 16, August 2019
DISCOVERY NOTE
SEQUENCE ANALYSIS
Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit
Justin R Klesmith and Benjamin J Hackel
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2707–2712, https://doi.org/10.1093/bioinformatics/bty1042
Linking sequence patterns and functionality of alpha-helical antimicrobial peptides
Igor E Eliseev and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2713–2717, https://doi.org/10.1093/bioinformatics/bty1048
SYSTEMS BIOLOGY
The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana
Tamir Tuller and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2718–2723, https://doi.org/10.1093/bioinformatics/bty1053
ORIGINAL PAPERS
GENOME ANALYSIS
Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps
L Carron and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2724–2729, https://doi.org/10.1093/bioinformatics/bty1059
Promoter analysis and prediction in the human genome using sequence-based deep learning models
Ramzan Umarov and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2730–2737, https://doi.org/10.1093/bioinformatics/bty1068
SEQUENCE ANALYSIS
The DNA walk and its demonstration of deterministic chaos—relevance to genomic alterations in lung cancer
Blake Hewelt and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2738–2748, https://doi.org/10.1093/bioinformatics/bty1021
PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization
Jialin Yu and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2749–2756, https://doi.org/10.1093/bioinformatics/bty1043
mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation
Balachandran Manavalan and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2757–2765, https://doi.org/10.1093/bioinformatics/bty1047
DeepPhos: prediction of protein phosphorylation sites with deep learning
Fenglin Luo and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2766–2773, https://doi.org/10.1093/bioinformatics/bty1051
MoMo: discovery of statistically significant post-translational modification motifs
Alice Cheng and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2774–2782, https://doi.org/10.1093/bioinformatics/bty1058
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity
Houxiang Zhu and Chun Liang
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2783–2789, https://doi.org/10.1093/bioinformatics/bty1061
DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences
Jan Ludwiczak and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2790–2795, https://doi.org/10.1093/bioinformatics/bty1062
i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome
Wei Chen and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2796–2800, https://doi.org/10.1093/bioinformatics/btz015
STRUCTURAL BIOINFORMATICS
Smooth orientation-dependent scoring function for coarse-grained protein quality assessment
Mikhail Karasikov and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2801–2808, https://doi.org/10.1093/bioinformatics/bty1037
GENE EXPRESSION
Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning
Xiangtao Li and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2809–2817, https://doi.org/10.1093/bioinformatics/bty1056
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing
Jinyan Chan and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2818–2826, https://doi.org/10.1093/bioinformatics/btz006
DATA AND TEXT MINING
CSHAP: efficient haplotype frequency estimation based on sparse representation
Yinsheng Zhou and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2827–2833, https://doi.org/10.1093/bioinformatics/bty1040
BIOIMAGE INFORMATICS
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model
Yang Yang and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2834–2842, https://doi.org/10.1093/bioinformatics/bty1064
APPLICATIONS NOTES
GENOME ANALYSIS
PINSPlus: a tool for tumor subtype discovery in integrated genomic data
Hung Nguyen and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2843–2846, https://doi.org/10.1093/bioinformatics/bty1049
ACE: absolute copy number estimation from low-coverage whole-genome sequencing data
Jos B Poell and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2847–2849, https://doi.org/10.1093/bioinformatics/bty1055
Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing
Georgette Tanner and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2850–2852, https://doi.org/10.1093/bioinformatics/bty1063
SEQUENCE ANALYSIS
GfaViz: flexible and interactive visualization of GFA sequence graphs
Giorgio Gonnella and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2853–2855, https://doi.org/10.1093/bioinformatics/bty1046
MMseqs2 desktop and local web server app for fast, interactive sequence searches
Milot Mirdita and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2856–2858, https://doi.org/10.1093/bioinformatics/bty1057
BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads
Linfang Jin and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2859–2861, https://doi.org/10.1093/bioinformatics/bty1070
STRUCTURAL BIOINFORMATICS
Integration of accessibility data from structure probing into RNA–RNA interaction prediction
Milad Miladi and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2862–2864, https://doi.org/10.1093/bioinformatics/bty1029
GENE EXPRESSION
M3Drop: dropout-based feature selection for scRNASeq
Tallulah S Andrews and Martin Hemberg
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2865–2867, https://doi.org/10.1093/bioinformatics/bty1044
GENETICS AND POPULATION ANALYSIS
polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species
Paula Tataru and Thomas Bataillon
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2868–2869, https://doi.org/10.1093/bioinformatics/bty1060
SYSTEMS BIOLOGY
MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery
Xiaotao Shen and Zheng-Jiang Zhu
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2870–2872, https://doi.org/10.1093/bioinformatics/bty1066
SIAN: software for structural identifiability analysis of ODE models
Hoon Hong and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2873–2874, https://doi.org/10.1093/bioinformatics/bty1069
Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein–protein interaction
Diego A A Morais and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2875–2876, https://doi.org/10.1093/bioinformatics/btz007
DATA AND TEXT MINING
Multiview: a software package for multiview pattern recognition methods
Samir Kanaan-Izquierdo and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2877–2879, https://doi.org/10.1093/bioinformatics/bty1039
Curse: building expression atlases and co-expression networks from public RNA-Seq data
Dries Vaneechoutte and Klaas Vandepoele
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2880–2881, https://doi.org/10.1093/bioinformatics/bty1052
DATABASES AND ONTOLOGIES
UbiHub: a data hub for the explorers of ubiquitination pathways
Lihua Liu and others
Bioinformatics, Volume 35, Issue 16, August 2019, Pages 2882–2884, https://doi.org/10.1093/bioinformatics/bty1067
CORRIGENDUM
Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization
Yuan Luo and others
Bioinformatics, Volume 35, Issue 16, August 2019, Page 2885, https://doi.org/10.1093/bioinformatics/btz049
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