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Volume 34, Issue 22, November 2018
ORIGINAL PAPERS
GENOME ANALYSIS
DeepMirTar: a deep-learning approach for predicting human miRNA targets
Ming Wen and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3781–3787, https://doi.org/10.1093/bioinformatics/bty424
Lost in translation: bioinformatic analysis of variations affecting the translation initiation codon in the human genome
Francisco Abad-Navarro and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3788–3794, https://doi.org/10.1093/bioinformatics/bty453
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data
Panisa Treepong and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3795–3800, https://doi.org/10.1093/bioinformatics/bty479
Bayesian integrative model for multi-omics data with missingness
Zhou Fang and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3801–3808, https://doi.org/10.1093/bioinformatics/bty775
SEQUENCE ANALYSIS
An automated method for detecting alternatively spliced protein domains
Vitor Coelho and Michael Sammeth
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3809–3816, https://doi.org/10.1093/bioinformatics/bty425
RIFRAF: a frame-resolving consensus algorithm
Kemal Eren and Ben Murrell
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3817–3824, https://doi.org/10.1093/bioinformatics/bty426
LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning
Cheng Yang and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3825–3834, https://doi.org/10.1093/bioinformatics/bty428
iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach
Bin Liu and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3835–3842, https://doi.org/10.1093/bioinformatics/bty458
PHYLOGENETICS
MASCOT: parameter and state inference under the marginal structured coalescent approximation
Nicola F Müller and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3843–3848, https://doi.org/10.1093/bioinformatics/bty406
STRUCTURAL BIOINFORMATICS
Knotty: efficient and accurate prediction of complex RNA pseudoknot structures
Hosna Jabbari and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3849–3856, https://doi.org/10.1093/bioinformatics/bty420
The size matters? A computational tool to design bivalent ligands
Laura Pérez-Benito and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3857–3863, https://doi.org/10.1093/bioinformatics/bty422
GENETICS AND POPULATION ANALYSIS
TriPoly: haplotype estimation for polyploids using sequencing data of related individuals
Ehsan Motazedi and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3864–3872, https://doi.org/10.1093/bioinformatics/bty442
SYSTEMS BIOLOGY
deepNF: deep network fusion for protein function prediction
Vladimir Gligorijević and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3873–3881, https://doi.org/10.1093/bioinformatics/bty440
Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis
Mingyuan Tian and Jennifer L Reed
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3882–3888, https://doi.org/10.1093/bioinformatics/bty445
DATA AND TEXT MINING
LncRNAnet: long non-coding RNA identification using deep learning
Junghwan Baek and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3889–3897, https://doi.org/10.1093/bioinformatics/bty418
An in silico proteomics screen to predict and prioritize protein–protein interactions dependent on post-translationally modified motifs
Anna M Schmoker and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3898–3906, https://doi.org/10.1093/bioinformatics/bty434
Predicting Cancer Drug Response using a Recommender System
Chayaporn Suphavilai and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3907–3914, https://doi.org/10.1093/bioinformatics/bty452
APPLICATIONS NOTES
GENOME ANALYSIS
TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data
Braulio Valdebenito-Maturana and Gonzalo Riadi
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3915–3916, https://doi.org/10.1093/bioinformatics/bty423
SciApps: a cloud-based platform for reproducible bioinformatics workflows
Liya Wang and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3917–3920, https://doi.org/10.1093/bioinformatics/bty439
ClusterScan: simple and generalistic identification of genomic clusters
Massimiliano Volpe and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3921–3923, https://doi.org/10.1093/bioinformatics/bty486
SEQUENCE ANALYSIS
Axe: rapid, competitive sequence read demultiplexing using a trie
Kevin D Murray and Justin O Borevitz
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3924–3925, https://doi.org/10.1093/bioinformatics/bty432
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files
Elisha D O Roberson
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3926–3928, https://doi.org/10.1093/bioinformatics/bty437
PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences
Simon Whelan and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3929–3930, https://doi.org/10.1093/bioinformatics/bty448
ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins
Sandeep Kumar Dhanda and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3931–3933, https://doi.org/10.1093/bioinformatics/bty463
Grimon: graphical interface to visualize multi-omics networks
Masahiro Kanai and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3934–3936, https://doi.org/10.1093/bioinformatics/bty488
ICBdocker: a Docker image for proteome annotation and visualization
Nicola Bordin and Damien P Devos
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3937–3938, https://doi.org/10.1093/bioinformatics/bty493
PASTA for proteins
Kodi Collins and Tandy Warnow
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3939–3941, https://doi.org/10.1093/bioinformatics/bty495
STRUCTURAL BIOINFORMATICS
BioStructMap: a Python tool for integration of protein structure and sequence-based features
Andrew J Guy and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3942–3944, https://doi.org/10.1093/bioinformatics/bty474
gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations
M Eric Irrgang and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3945–3947, https://doi.org/10.1093/bioinformatics/bty484
mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling
Joseph Masison and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3948–3950, https://doi.org/10.1093/bioinformatics/bty487
SYSTEMS BIOLOGY
ggCyto: next generation open-source visualization software for cytometry
Phu Van and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3951–3953, https://doi.org/10.1093/bioinformatics/bty441
iMetaLab 1.0: a web platform for metaproteomics data analysis
Bo Liao and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3954–3956, https://doi.org/10.1093/bioinformatics/bty466
DATA AND TEXT MINING
ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts
Teemu D Laajala and others
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3957–3959, https://doi.org/10.1093/bioinformatics/bty477
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