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Volume 35, Issue 24, December 2019
ORIGINAL PAPERS
GENOME ANALYSIS
MTTFsite: cross-cell type TF binding site prediction by using multi-task learning
Jiyun Zhou and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5067–5077, https://doi.org/10.1093/bioinformatics/btz451
New algorithms for detecting multi-effect and multi-way epistatic interactions
Javad Ansarifar and Lizhi Wang
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5078–5085, https://doi.org/10.1093/bioinformatics/btz463
SEQUENCE ANALYSIS
Full-length de novo viral quasispecies assembly through variation graph construction
Jasmijn A Baaijens and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5086–5094, https://doi.org/10.1093/bioinformatics/btz443
deconvSeq: deconvolution of cell mixture distribution in sequencing data
Rose Du and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5095–5102, https://doi.org/10.1093/bioinformatics/btz444
STRUCTURAL BIOINFORMATICS
DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data
Albert Y Xue and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5103–5112, https://doi.org/10.1093/bioinformatics/btz449
DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures
Guillaume Pagès and Sergei Grudinin
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5113–5120, https://doi.org/10.1093/bioinformatics/btz454
AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes
Yuqi Zhang and Michel F Sanner
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5121–5127, https://doi.org/10.1093/bioinformatics/btz459
DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network
Qiang Shi and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5128–5136, https://doi.org/10.1093/bioinformatics/btz464
GENE EXPRESSION
Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning
Onur Dereli and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5137–5145, https://doi.org/10.1093/bioinformatics/btz446
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
Joanna Zyla and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5146–5154, https://doi.org/10.1093/bioinformatics/btz447
DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data
Chengzhong Ye and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5155–5162, https://doi.org/10.1093/bioinformatics/btz453
GENETICS AND POPULATION ANALYSIS
Assessing concordance among human, in silico predictions and functional assays on genetic variant classification
Jiaqi Luo and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5163–5170, https://doi.org/10.1093/bioinformatics/btz442
SYSTEMS BIOLOGY
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification
Lara Schneider and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5171–5181, https://doi.org/10.1093/bioinformatics/btz302
Identification of disease-associated loci using machine learning for genotype and network data integration
Luis G Leal and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5182–5190, https://doi.org/10.1093/bioinformatics/btz310
deepDR: a network-based deep learning approach to in silico drug repositioning
Xiangxiang Zeng and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5191–5198, https://doi.org/10.1093/bioinformatics/btz418
Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning
Fredrik Wrede and Andreas Hellander
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5199–5206, https://doi.org/10.1093/bioinformatics/btz420
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures
Peilin Jia and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5207–5215, https://doi.org/10.1093/bioinformatics/btz441
A scalable method for parameter identification in kinetic models of metabolism using steady-state data
Shyam Srinivasan and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5216–5225, https://doi.org/10.1093/bioinformatics/btz445
Graphlet Laplacians for topology-function and topology-disease relationships
Sam F L Windels and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5226–5234, https://doi.org/10.1093/bioinformatics/btz455
DATA AND TEXT MINING
Deep learning of the back-splicing code for circular RNA formation
Jun Wang and Liangjiang Wang
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5235–5242, https://doi.org/10.1093/bioinformatics/btz382
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
Ana S C. Silva and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5243–5248, https://doi.org/10.1093/bioinformatics/btz383
ReSimNet: drug response similarity prediction using Siamese neural networks
Minji Jeon and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5249–5256, https://doi.org/10.1093/bioinformatics/btz411
Improving data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach
Camilo L M Morais and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5257–5263, https://doi.org/10.1093/bioinformatics/btz421
DATABASES AND ONTOLOGIES
A fully computational and reasonable representation for karyotypes
Jennifer D Warrender and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5264–5270, https://doi.org/10.1093/bioinformatics/btz440
BIOIMAGE INFORMATICS
Incorporating spatial–anatomical similarity into the VGWAS framework for AD biomarker detection
Meiyan Huang and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5271–5280, https://doi.org/10.1093/bioinformatics/btz401
ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques
Qi Shen and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5281–5289, https://doi.org/10.1093/bioinformatics/btz404
NRStitcher: non-rigid stitching of terapixel-scale volumetric images
Arttu Miettinen and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5290–5297, https://doi.org/10.1093/bioinformatics/btz423
APPLICATIONS NOTES
GENOME ANALYSIS
MEpurity: estimating tumor purity using DNA methylation data
Bowen Liu and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5298–5300, https://doi.org/10.1093/bioinformatics/btz555
Predicting promoters in phage genomes using PhagePromoter
Marta Sampaio and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5301–5302, https://doi.org/10.1093/bioinformatics/btz580
geneCo: a visualized comparative genomic method to analyze multiple genome structures
Jaehee Jung and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5303–5305, https://doi.org/10.1093/bioinformatics/btz596
scRNABatchQC: multi-samples quality control for single cell RNA-seq data
Qi Liu and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5306–5308, https://doi.org/10.1093/bioinformatics/btz601
SEQUENCE ANALYSIS
JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis
Ioannis A Tamposis and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5309–5312, https://doi.org/10.1093/bioinformatics/btz533
PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities
Thammakorn Saethang and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5313–5314, https://doi.org/10.1093/bioinformatics/btz568
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit
Maurits J J Dijkstra and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5315–5317, https://doi.org/10.1093/bioinformatics/btz572
Sequence tube maps: making graph genomes intuitive to commuters
Wolfgang Beyer and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5318–5320, https://doi.org/10.1093/bioinformatics/btz597
PHYLOGENETICS
MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees
Mark N Puttick
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5321–5322, https://doi.org/10.1093/bioinformatics/btz554
STRUCTURAL BIOINFORMATICS
TCR3d: The T cell receptor structural repertoire database
Ragul Gowthaman and Brian G Pierce
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5323–5325, https://doi.org/10.1093/bioinformatics/btz517
Benchmarking fold detection by DaliLite v.5
Liisa Holm
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5326–5327, https://doi.org/10.1093/bioinformatics/btz536
DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis
Simone Aureli and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5328–5330, https://doi.org/10.1093/bioinformatics/btz543
HDX-Viewer: interactive 3D visualization of hydrogen–deuterium exchange data
David Bouyssié and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5331–5333, https://doi.org/10.1093/bioinformatics/btz550
VeriNA3d: an R package for nucleic acids data mining
Diego Gallego and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5334–5336, https://doi.org/10.1093/bioinformatics/btz553
diSTruct v1.0: generating biomolecular structures from distance constraints
Oskar Taubert and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5337–5338, https://doi.org/10.1093/bioinformatics/btz578
GENE EXPRESSION
TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets
Laura Puente-Santamaria and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5339–5340, https://doi.org/10.1093/bioinformatics/btz573
GENETICS AND POPULATION ANALYSIS
CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data
Yeongjun Jang and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5341–5343, https://doi.org/10.1093/bioinformatics/btz516
Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages
Carles Hernandez-Ferrer and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5344–5345, https://doi.org/10.1093/bioinformatics/btz526
Genetic association testing using the GENESIS R/Bioconductor package
Stephanie M Gogarten and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5346–5348, https://doi.org/10.1093/bioinformatics/btz567
amplimap: a versatile tool to process and analyze targeted NGS data
Nils Koelling and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5349–5350, https://doi.org/10.1093/bioinformatics/btz582
MPRAscore: robust and non-parametric analysis of massively parallel reporter assays
Abhishek Niroula and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5351–5353, https://doi.org/10.1093/bioinformatics/btz591
SYSTEMS BIOLOGY
KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules
Zhaojun Li and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5354–5356, https://doi.org/10.1093/bioinformatics/btz519
RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons
Vinicius S Chagas and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5357–5358, https://doi.org/10.1093/bioinformatics/btz534
The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets
Caroline J Sands and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5359–5360, https://doi.org/10.1093/bioinformatics/btz566
CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models
Vítor Vieira and Miguel Rocha
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5361–5362, https://doi.org/10.1093/bioinformatics/btz598
BLANT—fast graphlet sampling tool
Sridevi Maharaj and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5363–5364, https://doi.org/10.1093/bioinformatics/btz603
DATA AND TEXT MINING
CytoGPS: a web-enabled karyotype analysis tool for cytogenetics
Zachary B Abrams and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5365–5366, https://doi.org/10.1093/bioinformatics/btz520
The NEW ESID online database network
Raphael Scheible and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5367–5369, https://doi.org/10.1093/bioinformatics/btz525
VariantQC: a visual quality control report for variant evaluation
Melissa Y Yan and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5370–5371, https://doi.org/10.1093/bioinformatics/btz560
SquiggleKit: a toolkit for manipulating nanopore signal data
James M Ferguson and Martin A Smith
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5372–5373, https://doi.org/10.1093/bioinformatics/btz586
DISPOT: a simple knowledge-based protein domain interaction statistical potential
Oleksandr Narykov and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5374–5378, https://doi.org/10.1093/bioinformatics/btz587
PyMethylProcess—convenient high-throughput preprocessing workflow for DNA methylation data
Joshua J Levy and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5379–5381, https://doi.org/10.1093/bioinformatics/btz594
ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering
Kenneth Morton and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5382–5384, https://doi.org/10.1093/bioinformatics/btz604
DATABASES AND ONTOLOGIES
Interactive exploration of heterogeneous biological networks with Biomine Explorer
Vid Podpečan and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5385–5388, https://doi.org/10.1093/bioinformatics/btz509
ValTrendsDB: bringing Protein Data Bank validation information closer to the user
Vladimír Horský and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5389–5390, https://doi.org/10.1093/bioinformatics/btz532
sAOP: linking chemical stressors to adverse outcomes pathway networks
Alejandro Aguayo-Orozco and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5391–5392, https://doi.org/10.1093/bioinformatics/btz570
BIOIMAGE INFORMATICS
Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers
Eric Wait and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5393–5395, https://doi.org/10.1093/bioinformatics/btz523
CORRIGENDA
OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers
Claudia Arnedo-Pac and others
Bioinformatics, Volume 35, Issue 24, December 2019, Page 5396, https://doi.org/10.1093/bioinformatics/btz588
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome
Anjun Ma and others
Bioinformatics, Volume 35, Issue 24, December 2019, Page 5397, https://doi.org/10.1093/bioinformatics/btz696
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