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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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SYSTEMS BIOLOGY

ClinOmicsTrail^bc: 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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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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