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Volume 36, Issue 1, January 2020
ORIGINAL PAPERS
GENOME ANALYSIS
Cloud bursting galaxy: federated identity and access management
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 1–9, https://doi.org/10.1093/bioinformatics/btz472
MRLR: unraveling high-resolution meiotic recombination by linked reads
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 10–16, https://doi.org/10.1093/bioinformatics/btz503
Bayesian GWAS with Structured and Non-Local Priors
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 17–25, https://doi.org/10.1093/bioinformatics/btz518
SEQUENCE ANALYSIS
DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 26–32, https://doi.org/10.1093/bioinformatics/btz473
arcasHLA: high-resolution HLA typing from RNAseq
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 33–40, https://doi.org/10.1093/bioinformatics/btz474
Protein contact prediction using metagenome sequence data and residual neural networks
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 41–48, https://doi.org/10.1093/bioinformatics/btz477
sefOri: selecting the best-engineered sequence features to predict DNA replication origins
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 49–55, https://doi.org/10.1093/bioinformatics/btz506
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 56–64, https://doi.org/10.1093/bioinformatics/btz512
Simultaneous prediction of multiple outcomes using revised stacking algorithms
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 65–72, https://doi.org/10.1093/bioinformatics/btz531
circDeep: deep learning approach for circular RNA classification from other long non-coding RNA
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 73–80, https://doi.org/10.1093/bioinformatics/btz537
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 81–89, https://doi.org/10.1093/bioinformatics/btz541
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 90–95, https://doi.org/10.1093/bioinformatics/btz552
STRUCTURAL BIOINFORMATICS
P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 96–103, https://doi.org/10.1093/bioinformatics/btz478
Sequence alignment using machine learning for accurate template-based protein structure prediction
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 104–111, https://doi.org/10.1093/bioinformatics/btz483
iScore: a novel graph kernel-based function for scoring protein–protein docking models
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 112–121, https://doi.org/10.1093/bioinformatics/btz496
Positive multistate protein design
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 122–130, https://doi.org/10.1093/bioinformatics/btz497
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 131–135, https://doi.org/10.1093/bioinformatics/btz502
Increasing the efficiency and accuracy of the ABACUS protein sequence design method
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 136–144, https://doi.org/10.1093/bioinformatics/btz515
MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 145–153, https://doi.org/10.1093/bioinformatics/btz521
A helical lock and key model of polyproline II conformation with SH3
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 154–159, https://doi.org/10.1093/bioinformatics/btz527
Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 160–168, https://doi.org/10.1093/bioinformatics/btz538
GENE EXPRESSION
A dynamic programing approach to integrate gene expression data and network information for pathway model generation
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 169–176, https://doi.org/10.1093/bioinformatics/btz467
An empirical Bayesian ranking method, with applications to high throughput biology
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 177–185, https://doi.org/10.1093/bioinformatics/btz471
Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington’s disease mice synchronous to symptoms
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 186–196, https://doi.org/10.1093/bioinformatics/btz514
Inference of differential gene regulatory networks based on gene expression and genetic perturbation data
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 197–204, https://doi.org/10.1093/bioinformatics/btz529
MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 205–211, https://doi.org/10.1093/bioinformatics/btz530
GENETICS AND POPULATION ANALYSIS
Mycorrhiza: genotype assignment using phylogenetic networks
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 212–220, https://doi.org/10.1093/bioinformatics/btz476
Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 221–231, https://doi.org/10.1093/bioinformatics/btz498
SYSTEMS BIOLOGY
Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 232–240, https://doi.org/10.1093/bioinformatics/btz500
Modelling cancer progression using Mutual Hazard Networks
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 241–249, https://doi.org/10.1093/bioinformatics/btz513
DATA AND TEXT MINING
Scaling tree-based automated machine learning to biomedical big data with a feature set selector
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 250–256, https://doi.org/10.1093/bioinformatics/btz470
GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 257–263, https://doi.org/10.1093/bioinformatics/btz488
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 264–271, https://doi.org/10.1093/bioinformatics/btz490
Deep learning on chaos game representation for proteins
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 272–279, https://doi.org/10.1093/bioinformatics/btz493
Towards reliable named entity recognition in the biomedical domain
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 280–286, https://doi.org/10.1093/bioinformatics/btz504
Deep representation learning for domain adaptable classification of infrared spectral imaging data
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 287–294, https://doi.org/10.1093/bioinformatics/btz505
HUNER: improving biomedical NER with pretraining
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 295–302, https://doi.org/10.1093/bioinformatics/btz528
Isoform function prediction based on bi-random walks on a heterogeneous network
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 303–310, https://doi.org/10.1093/bioinformatics/btz535
Cooler: scalable storage for Hi-C data and other genomically labeled arrays
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 311–316, https://doi.org/10.1093/bioinformatics/btz540
BIOIMAGE INFORMATICS
A sequential algorithm to detect diffusion switching along intracellular particle trajectories
Bioinformatics, Volume 36, Issue 1, January 2020, Pages 317–329, https://doi.org/10.1093/bioinformatics/btz489
ERRATUM
Adaptive boosting-based computational model for predicting potential miRNA-disease associations
Bioinformatics, Volume 36, Issue 1, January 2020, Page 330, https://doi.org/10.1093/bioinformatics/btz475
