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Volume 35, Issue 21, 1 November 2019
ORIGINAL PAPERS
GENOME ANALYSIS
TORMES: an automated pipeline for whole bacterial genome analysis
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4207–4212, https://doi.org/10.1093/bioinformatics/btz220
Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4213–4221, https://doi.org/10.1093/bioinformatics/btz241
HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4222–4228, https://doi.org/10.1093/bioinformatics/btz251
SolidBin: improving metagenome binning with semi-supervised normalized cut
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4229–4238, https://doi.org/10.1093/bioinformatics/btz253
SEQUENCE ANALYSIS
Graph analysis of fragmented long-read bacterial genome assemblies
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4239–4246, https://doi.org/10.1093/bioinformatics/btz219
A Bayesian model integration for mutation calling through data partitioning
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4247–4254, https://doi.org/10.1093/bioinformatics/btz233
Shouji: a fast and efficient pre-alignment filter for sequence alignment
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4255–4263, https://doi.org/10.1093/bioinformatics/btz234
scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4264–4271, https://doi.org/10.1093/bioinformatics/btz240
PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4272–4280, https://doi.org/10.1093/bioinformatics/btz246
Overlap graph-based generation of haplotigs for diploids and polyploids
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4281–4289, https://doi.org/10.1093/bioinformatics/btz255
PHYLOGENETICS
Accounting for ambiguity in ancestral sequence reconstruction
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4290–4297, https://doi.org/10.1093/bioinformatics/btz249
STRUCTURAL BIOINFORMATICS
Determining parameters for non-linear models of multi-loop free energy change
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4298–4306, https://doi.org/10.1093/bioinformatics/btz222
GENE EXPRESSION
Assessing reproducibility of matrix factorization methods in independent transcriptomes
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4307–4313, https://doi.org/10.1093/bioinformatics/btz225
Performance of gene expression analyses using de novo assembled transcripts in polyploid species
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4314–4320, https://doi.org/10.1093/bioinformatics/btz620
GENETICS AND POPULATION ANALYSIS
Kinpute: using identity by descent to improve genotype imputation
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4321–4326, https://doi.org/10.1093/bioinformatics/btz221
A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4327–4335, https://doi.org/10.1093/bioinformatics/btz244
SYSTEMS BIOLOGY
Unsupervised discovery of phenotype-specific multi-omics networks
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4336–4343, https://doi.org/10.1093/bioinformatics/btz226
Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4344–4349, https://doi.org/10.1093/bioinformatics/btz230
rMTA: robust metabolic transformation analysis
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4350–4355, https://doi.org/10.1093/bioinformatics/btz231
ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4356–4363, https://doi.org/10.1093/bioinformatics/btz248
A learning-based framework for miRNA-disease association identification using neural networks
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4364–4371, https://doi.org/10.1093/bioinformatics/btz254
DATA AND TEXT MINING
Open Agile text mining for bioinformatics: the PubAnnotation ecosystem
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4372–4380, https://doi.org/10.1093/bioinformatics/btz227
Figure and caption extraction from biomedical documents
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4381–4388, https://doi.org/10.1093/bioinformatics/btz228
APPLICATIONS NOTES
GENOME ANALYSIS
GenomeWarp: an alignment-based variant coordinate transformation
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4389–4391, https://doi.org/10.1093/bioinformatics/btz218
epic2 efficiently finds diffuse domains in ChIP-seq data
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4392–4393, https://doi.org/10.1093/bioinformatics/btz232
HLA*LA—HLA typing from linearly projected graph alignments
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4394–4396, https://doi.org/10.1093/bioinformatics/btz235
Structural variant analysis for linked-read sequencing data with gemtools
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4397–4399, https://doi.org/10.1093/bioinformatics/btz239
IntronDB: a database for eukaryotic intron features
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4400–4401, https://doi.org/10.1093/bioinformatics/btz242
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4402–4404, https://doi.org/10.1093/bioinformatics/btz258
Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4405–4407, https://doi.org/10.1093/bioinformatics/btz263
Identifying centromeric satellites with dna-brnn
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4408–4410, https://doi.org/10.1093/bioinformatics/btz264
icHET: interactive visualization of cytoplasmic heteroplasmy
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4411–4412, https://doi.org/10.1093/bioinformatics/btz300
Graphical data mining of cancer mechanisms with SEMA
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4413–4418, https://doi.org/10.1093/bioinformatics/btz303
gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4419–4421, https://doi.org/10.1093/bioinformatics/btz308
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4422–4423, https://doi.org/10.1093/bioinformatics/btz309
Tibanna: software for scalable execution of portable pipelines on the cloud
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4424–4426, https://doi.org/10.1093/bioinformatics/btz379
Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4427–4429, https://doi.org/10.1093/bioinformatics/btz380
ntEdit: scalable genome sequence polishing
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4430–4432, https://doi.org/10.1093/bioinformatics/btz400
TPES: tumor purity estimation from SNVs
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4433–4435, https://doi.org/10.1093/bioinformatics/btz406
HyAsP, a greedy tool for plasmids identification
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4436–4439, https://doi.org/10.1093/bioinformatics/btz413
SPar-K: a method to partition NGS signal data
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4440–4441, https://doi.org/10.1093/bioinformatics/btz416
simuG: a general-purpose genome simulator
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4442–4444, https://doi.org/10.1093/bioinformatics/btz424
SEQUENCE ANALYSIS
PyPore: a python toolbox for nanopore sequencing data handling
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4445–4447, https://doi.org/10.1093/bioinformatics/btz269
ORCA: a comprehensive bioinformatics container environment for education and research
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4448–4450, https://doi.org/10.1093/bioinformatics/btz278
Cram-JS: reference-based decompression in node and the browser
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4451–4452, https://doi.org/10.1093/bioinformatics/btz384
PHYLOGENETICS
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4453–4455, https://doi.org/10.1093/bioinformatics/btz305
STRUCTURAL BIOINFORMATICS
parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4456–4458, https://doi.org/10.1093/bioinformatics/btz224
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4459–4461, https://doi.org/10.1093/bioinformatics/btz282
epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4462–4464, https://doi.org/10.1093/bioinformatics/btz387
GENE EXPRESSION
FusionLearn: a biomarker selection algorithm on cross-platform data
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4465–4468, https://doi.org/10.1093/bioinformatics/btz223
IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4469–4471, https://doi.org/10.1093/bioinformatics/btz247
The barcode, UMI, set format and BUStools
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4472–4473, https://doi.org/10.1093/bioinformatics/btz279
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4474–4477, https://doi.org/10.1093/bioinformatics/btz414
GENETICS AND POPULATION ANALYSIS
Variant Score Ranker—a web application for intuitive missense variant prioritization
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4478–4479, https://doi.org/10.1093/bioinformatics/btz252
SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4480–4483, https://doi.org/10.1093/bioinformatics/btz311
SYSTEMS BIOLOGY
IsoCor: isotope correction for high-resolution MS labeling experiments
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4484–4487, https://doi.org/10.1093/bioinformatics/btz209
RTNsurvival: an R/Bioconductor package for regulatory network survival analysis
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4488–4489, https://doi.org/10.1093/bioinformatics/btz229
The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein–protein interaction and signalling networks
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4490–4492, https://doi.org/10.1093/bioinformatics/btz257
clustermq enables efficient parallelization of genomic analyses
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4493–4495, https://doi.org/10.1093/bioinformatics/btz284
MINERVA API and plugins: opening molecular network analysis and visualization to the community
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4496–4498, https://doi.org/10.1093/bioinformatics/btz286
sbgntikz—a TikZ library to draw SBGN maps
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4499–4500, https://doi.org/10.1093/bioinformatics/btz287
INDRA-IPM: interactive pathway modeling using natural language with automated assembly
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4501–4503, https://doi.org/10.1093/bioinformatics/btz289
PathFXweb: a web application for identifying drug safety and efficacy phenotypes
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4504–4506, https://doi.org/10.1093/bioinformatics/btz419
DATA AND TEXT MINING
Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4507–4508, https://doi.org/10.1093/bioinformatics/btz250
TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4509–4510, https://doi.org/10.1093/bioinformatics/btz270
Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4511–4514, https://doi.org/10.1093/bioinformatics/btz385
PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4515–4518, https://doi.org/10.1093/bioinformatics/btz409
DATABASES AND ONTOLOGIES
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4519–4521, https://doi.org/10.1093/bioinformatics/btz245
BIOIMAGE INFORMATICS
Biomedical image augmentation using Augmentor
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4522–4524, https://doi.org/10.1093/bioinformatics/btz259
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4525–4527, https://doi.org/10.1093/bioinformatics/btz402
MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4528–4530, https://doi.org/10.1093/bioinformatics/btz403
CytoPacq: a web-interface for simulating multi-dimensional cell imaging
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4531–4533, https://doi.org/10.1093/bioinformatics/btz417
CORRIGENDA
Haplotype assembly of autotetraploid potato using integer linear programing
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Page 4534, https://doi.org/10.1093/bioinformatics/btz511
PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Page 4535, https://doi.org/10.1093/bioinformatics/btz546
Nanopype: a modular and scalable nanopore data processing pipeline
Bioinformatics, Volume 35, Issue 21, 1 November 2019, Page 4536, https://doi.org/10.1093/bioinformatics/btz547
