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Volume 36, Issue 2, January 2020
ORIGINAL PAPERS
GENOME ANALYSIS
Bayesian estimation of genetic regulatory effects in high-throughput reporter assays
William H Majoros and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 331–338, https://doi.org/10.1093/bioinformatics/btz545
Identification of expression signatures for non-small-cell lung carcinoma subtype classification
Ran Su and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 339–346, https://doi.org/10.1093/bioinformatics/btz557
Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data
Chan Wang and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 347–355, https://doi.org/10.1093/bioinformatics/btz565
MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies
Terry Ma and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 356–363, https://doi.org/10.1093/bioinformatics/btz577
Predicting the effects of SNPs on transcription factor binding affinity
Sierra S Nishizaki and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 364–372, https://doi.org/10.1093/bioinformatics/btz612
ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads
Patrick Sorn and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 373–379, https://doi.org/10.1093/bioinformatics/btz613
SEQUENCE ANALYSIS
Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models
Alfredo Velasco and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 380–387, https://doi.org/10.1093/bioinformatics/btz551
MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model
Cong Pian and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 388–392, https://doi.org/10.1093/bioinformatics/btz556
QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable
Michele Berselli and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 393–399, https://doi.org/10.1093/bioinformatics/btz569
Haplotype-aware graph indexes
Jouni Sirén and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 400–407, https://doi.org/10.1093/bioinformatics/btz575
How sequence alignment scores correspond to probability models
Martin C Frith
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 408–415, https://doi.org/10.1093/bioinformatics/btz576
THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage
Chloé Dimeglio and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 416–421, https://doi.org/10.1093/bioinformatics/btz585
DeepGOPlus: improved protein function prediction from sequence
Maxat Kulmanov and Robert Hoehndorf
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 422–429, https://doi.org/10.1093/bioinformatics/btz595
PHYLOGENETICS
The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation
Roberto Del Amparo and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 430–436, https://doi.org/10.1093/bioinformatics/btz558
STRUCTURAL BIOINFORMATICS
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement
Di Wang and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 437–448, https://doi.org/10.1093/bioinformatics/btz544
DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing
Justin Chan and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 449–461, https://doi.org/10.1093/bioinformatics/btz579
pourRNA—a time- and memory-efficient approach for the guided exploration of RNA energy landscapes
Gregor Entzian and Martin Raden
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 462–469, https://doi.org/10.1093/bioinformatics/btz583
DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout
Badri Adhikari
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 470–477, https://doi.org/10.1093/bioinformatics/btz593
Topology-independent and global protein structure alignment through an FFT-based algorithm
Zeyu Wen and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 478–486, https://doi.org/10.1093/bioinformatics/btz609
GENE EXPRESSION
GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis
Adib Shafi and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 487–495, https://doi.org/10.1093/bioinformatics/btz561
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network
Wanwen Zeng and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 496–503, https://doi.org/10.1093/bioinformatics/btz562
ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses
Christelle Reynès and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 504–513, https://doi.org/10.1093/bioinformatics/btz564
MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network
Taneli Pusa and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 514–523, https://doi.org/10.1093/bioinformatics/btz584
P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher’s meta-analysis method in omics applications
Zhiguang Huo and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 524–532, https://doi.org/10.1093/bioinformatics/btz589
ACTINN: automated identification of cell types in single cell RNA sequencing
Feiyang Ma and Matteo Pellegrini
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 533–538, https://doi.org/10.1093/bioinformatics/btz592
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs
Li Chen and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 539–545, https://doi.org/10.1093/bioinformatics/btz606
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data
Kyungsoo Kim and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 546–551, https://doi.org/10.1093/bioinformatics/btz610
GENETICS AND POPULATION ANALYSIS
Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease
Lerato E Magosi and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 552–557, https://doi.org/10.1093/bioinformatics/btz590
SYSTEMS BIOLOGY
Comparison of single and module-based methods for modeling gene regulatory networks
Mikel Hernaez and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 558–567, https://doi.org/10.1093/bioinformatics/btz549
Identifying emerging phenomenon in long temporal phenotyping experiments
Jiajie Peng and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 568–577, https://doi.org/10.1093/bioinformatics/btz559
ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics
Ning Shi and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 578–585, https://doi.org/10.1093/bioinformatics/btz563
Bayesian inference of distributed time delay in transcriptional and translational regulation
Boseung Choi and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 586–593, https://doi.org/10.1093/bioinformatics/btz574
Efficient parameterization of large-scale dynamic models based on relative measurements
Leonard Schmiester and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 594–602, https://doi.org/10.1093/bioinformatics/btz581
Discovering protein drug targets using knowledge graph embeddings
Sameh K Mohamed and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 603–610, https://doi.org/10.1093/bioinformatics/btz600
DATA AND TEXT MINING
BioNorm: deep learning-based event normalization for the curation of reaction databases
Peiliang Lou and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 611–620, https://doi.org/10.1093/bioinformatics/btz571
Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping
Siva Rajesh Kasa and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 621–628, https://doi.org/10.1093/bioinformatics/btz599
Non-parametric individual treatment effect estimation for survival data with random forests
Sami Tabib and Denis Larocque
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 629–636, https://doi.org/10.1093/bioinformatics/btz602
Context awareness and embedding for biomedical event extraction
Shankai Yan and Ka-Chun Wong
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 637–643, https://doi.org/10.1093/bioinformatics/btz607
APPLICATIONS NOTES
GENOME ANALYSIS
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data
R N Ramirez and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 644–646, https://doi.org/10.1093/bioinformatics/btz608
STRUCTURAL BIOINFORMATICS
RAG-Web: RNA structure prediction/design using RNA-As-Graphs
Grace Meng and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 647–648, https://doi.org/10.1093/bioinformatics/btz611
DATA AND TEXT MINING
gwasrapidd: an R package to query, download and wrangle GWAS catalog data
Ramiro Magno and Ana-Teresa Maia
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 649–650, https://doi.org/10.1093/bioinformatics/btz605
CORRIGENDUM
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
Antoine Limasset and others
Bioinformatics, Volume 36, Issue 2, January 2020, Page 651, https://doi.org/10.1093/bioinformatics/btz548
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