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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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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