Advance articles
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Brief Report 29 July 2017
FAF-Drugs4: Free ADME-Tox Filtering computations for chemical biology and early stages drug discovery
Bioinformatics, btx491, 10.1093/bioinformatics/btx491Published: 29 July 2017 Section: APPLICATIONS NOTE -
Research Article 29 July 2017
Improved prediction of breast cancer outcome by identifying heterogeneous biomarkers
Bioinformatics, btx487, 10.1093/bioinformatics/btx487Published: 29 July 2017 Section: Original Paper -
Research Article 29 July 2017
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise
Bioinformatics, btx482, 10.1093/bioinformatics/btx482Published: 29 July 2017 Section: Original Paper -
Brief Report 28 July 2017
4D Nucleome Analysis Toolbox: Analysis of Hi-C data with abnormal karyotype and time series capabilities
Bioinformatics, btx484, 10.1093/bioinformatics/btx484Published: 28 July 2017 Section: APPLICATIONS NOTE -
Brief Report 28 July 2017
3DBIONOTES v2.0: A web server for the automatic annotation of macromolecular structures
Bioinformatics, btx483, 10.1093/bioinformatics/btx483Published: 28 July 2017 Section: APPLICATIONS NOTE -
Research Article 27 July 2017
Predicting Novel Metabolic Pathways through Subgraph Mining
Bioinformatics, btx481, 10.1093/bioinformatics/btx481Published: 27 July 2017 Section: Original Paper -
Research Article 27 July 2017
Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape
Bioinformatics, btx480, 10.1093/bioinformatics/btx480Published: 27 July 2017 Section: Original Paper -
Brief Report 27 July 2017
pgRNAFinder: a web-based tool to design distance independent paired-gRNA
Bioinformatics, btx472, 10.1093/bioinformatics/btx472Published: 27 July 2017 Section: APPLICATIONS NOTE -
Research Article 26 July 2017
iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties
Bioinformatics, btx479, 10.1093/bioinformatics/btx479Published: 26 July 2017 Section: Original Paper -
Brief Report 26 July 2017
MWASTools: an R/Bioconductor package for metabolome-wide association studies
Bioinformatics, btx477, 10.1093/bioinformatics/btx477Published: 26 July 2017 Section: APPLICATIONS NOTE -
Research Article 26 July 2017
Cloud-based Interactive Analytics for Terabytes of Genomic Variants Data
Bioinformatics, btx468, 10.1093/bioinformatics/btx468Published: 26 July 2017 Section: Original Paper -
Research Article 26 July 2017
Towards Clinically More Relevant Dissection of Patient Heterogeneity via Survival based Bayesian Clustering
Bioinformatics, btx464, 10.1093/bioinformatics/btx464Published: 26 July 2017 Section: Original Paper -
Brief Report 24 July 2017
CrocoBLAST: Running BLAST Efficiently in the Age of Next-Generation Sequencing
Ravi José Tristão Ramos; Allan Cézar de Azevedo Martins; Gabrielle da Silva Delgado; Crina-Maria Ionescu; Turán Peter Ürményi ...Bioinformatics, btx465, 10.1093/bioinformatics/btx465Published: 24 July 2017 Section: APPLICATIONS NOTE -
Research Article 24 July 2017
pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites
Bioinformatics, btx476, 10.1093/bioinformatics/btx476Published: 24 July 2017 Section: Original Paper -
Brief Report 24 July 2017
myVCF: a desktop application for high-throughput mutations data management
Bioinformatics, btx475, 10.1093/bioinformatics/btx475Published: 24 July 2017 Section: APPLICATIONS NOTE -
Research Article 24 July 2017
SPRINT: A SNP-free toolkit for identifying RNA editing sites
Bioinformatics, btx473, 10.1093/bioinformatics/btx473Published: 24 July 2017 Section: Original Paper -
Research Article 24 July 2017
Faucet: streaming de novo assembly graph construction
Bioinformatics, btx471, 10.1093/bioinformatics/btx471Published: 24 July 2017 Section: Original Paper -
Research Article 24 July 2017
Using uncertainty to link and rank evidence from biomedical literature for model curation
Bioinformatics, btx466, 10.1093/bioinformatics/btx466Published: 24 July 2017 Section: Original Paper -
Brief Report 24 July 2017
wft4galaxy: A Workflow Testing Tool for Galaxy
Bioinformatics, btx461, 10.1093/bioinformatics/btx461Published: 24 July 2017 Section: APPLICATIONS NOTE -
Research Article 21 July 2017
Mechanisms to Protect the Privacy of Families when Using the Transmission Disequilibrium Test in Genome-Wide Association Studies
Bioinformatics, btx470, 10.1093/bioinformatics/btx470Published: 21 July 2017 Section: Original Paper -
Brief Report 21 July 2017
PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes
Bioinformatics, btx462, 10.1093/bioinformatics/btx462Published: 21 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 21 July 2017
PySeqLab: an open source Python package for sequence labeling and segmentation
Bioinformatics, btx451, 10.1093/bioinformatics/btx451Published: 21 July 2017 Section: APPLICATIONS NOTE -
Brief Report 20 July 2017
ggseqlogo: a versatile R package for drawing sequence logos
Bioinformatics, btx469, 10.1093/bioinformatics/btx469Published: 20 July 2017 Section: APPLICATIONS NOTE -
Research Article 20 July 2017
Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data
Bioinformatics, btx467, 10.1093/bioinformatics/btx467Published: 20 July 2017 Section: Original Paper -
Research Article 20 July 2017
FOLD: A method to optimize power in meta-analysis of genetic association studies with overlapping subjects
Bioinformatics, btx463, 10.1093/bioinformatics/btx463Published: 20 July 2017 Section: Original Paper -
Corrected Proof
Research Article 20 July 2017
Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array
Bioinformatics, btx372, 10.1093/bioinformatics/btx372Published: 20 July 2017 Section: Original Paper -
Corrected Proof
Research Article 20 July 2017
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules
Bioinformatics, btx344, 10.1093/bioinformatics/btx344Published: 20 July 2017 Section: Original Paper -
Brief Report 18 July 2017
Phylotyper: In silico predictor of gene subtypes
Bioinformatics, btx459, 10.1093/bioinformatics/btx459Published: 18 July 2017 Section: APPLICATIONS NOTE -
Brief Report 17 July 2017
SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces
Bioinformatics, btx456, 10.1093/bioinformatics/btx456Published: 17 July 2017 Section: APPLICATIONS NOTE -
Research Article 14 July 2017
Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology
Bioinformatics, btx460, 10.1093/bioinformatics/btx460Published: 14 July 2017 Section: Original Paper -
Research Article 14 July 2017
proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry
Bioinformatics, btx458, 10.1093/bioinformatics/btx458Published: 14 July 2017 Section: Original Paper -
Research Article 14 July 2017
A robust DF-REML framework for variance components estimation in genetic studies
Bioinformatics, btx457, 10.1093/bioinformatics/btx457Published: 14 July 2017 Section: Original Paper -
Research Article 14 July 2017
SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms
Bioinformatics, btx455, 10.1093/bioinformatics/btx455Published: 14 July 2017 Section: Original Paper -
Research Article 14 July 2017
Cancer Hallmarks Analytics Tool (CHAT):A text mining approach to organise and evaluate scientific literature on cancer
Bioinformatics, btx454, 10.1093/bioinformatics/btx454Published: 14 July 2017 Section: Original Paper -
Research Article 14 July 2017
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models
Bioinformatics, btx453, 10.1093/bioinformatics/btx453Published: 14 July 2017 Section: Original Paper -
Corrected Proof
Brief Report 14 July 2017
ScanGEO: parallel mining of high-throughput gene expression data
Bioinformatics, btx452, 10.1093/bioinformatics/btx452Published: 14 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 14 July 2017
VariantTools: an extensible framework for developing and testing variant callers
Bioinformatics, btx450, 10.1093/bioinformatics/btx450Published: 14 July 2017 Section: APPLICATIONS NOTE -
Research Article 14 July 2017
Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data
Bioinformatics, btx442, 10.1093/bioinformatics/btx442Published: 14 July 2017 Section: Original Paper -
Corrected Proof
Brief Report 13 July 2017
MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor
Bioinformatics, btx449, 10.1093/bioinformatics/btx449Published: 13 July 2017 Section: APPLICATIONS NOTE -
Research Article 13 July 2017
Gating Mass Cytometry Data by Deep Learning
Bioinformatics, btx448, 10.1093/bioinformatics/btx448Published: 13 July 2017 Section: Original Paper -
Brief Report 13 July 2017
cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations
Bioinformatics, btx444, 10.1093/bioinformatics/btx444Published: 13 July 2017 Section: APPLICATIONS NOTE -
Research Article 13 July 2017
On expert curation and scalability:UniProtKB/Swiss-Prot as a case study
Bioinformatics, btx439, 10.1093/bioinformatics/btx439Published: 13 July 2017 Section: Original Paper -
Brief Report 13 July 2017
GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data
Bioinformatics, btx423, 10.1093/bioinformatics/btx423Published: 13 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 13 July 2017
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
Bioinformatics, btx383, 10.1093/bioinformatics/btx383Published: 13 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 12 July 2017
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential
Bioinformatics, btx446, 10.1093/bioinformatics/btx446Published: 12 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Research Article 12 July 2017
StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data
Elena D. Stavrovskaya; Tejasvi Niranjan; Elana J. Fertig; Sarah J. Wheelan; Alexander V. Favorov ...Bioinformatics, btx379, 10.1093/bioinformatics/btx379Published: 12 July 2017 Section: Original Paper -
Corrected Proof
Correction 11 July 2017
Kollector: transcript-informed, targeted de novo assembly of gene loci
Bioinformatics, btx405, 10.1093/bioinformatics/btx405Published: 11 July 2017 Section: Corrigendum -
Corrected Proof
Brief Report 11 July 2017
TeachEnG: a Teaching Engine for Genomics
Bioinformatics, btx447, 10.1093/bioinformatics/btx447Published: 11 July 2017 Section: APPLICATIONS NOTE -
Brief Report 11 July 2017
Irys Extract
Bioinformatics, btx437, 10.1093/bioinformatics/btx437Published: 11 July 2017 Section: APPLICATIONS NOTE -
Research Article 11 July 2017
An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments
Bioinformatics, btx436, 10.1093/bioinformatics/btx436Published: 11 July 2017 Section: Original Paper -
Brief Report 11 July 2017
powsimR: Power analysis for bulk and single cell RNA-seq experiments
Bioinformatics, btx435, 10.1093/bioinformatics/btx435Published: 11 July 2017 Section: APPLICATIONS NOTE -
Brief Report 11 July 2017
nandb—number and brightness in R with a novel automatic detrending algorithm
Bioinformatics, btx434, 10.1093/bioinformatics/btx434Published: 11 July 2017 Section: APPLICATIONS NOTE -
Brief Report 7 July 2017
gVolante for standardizing completeness assessment of genome and transcriptome assemblies
Bioinformatics, btx445, 10.1093/bioinformatics/btx445Published: 7 July 2017 Section: APPLICATIONS NOTE -
Brief Report 7 July 2017
DynaPho: a web platform for inferring the dynamics of time-series phosphoproteomics
Bioinformatics, btx443, 10.1093/bioinformatics/btx443Published: 7 July 2017 Section: APPLICATIONS NOTE -
Research Article 7 July 2017
VICTOR: Genome-based Phylogeny and Classification of Prokaryotic Viruses
Bioinformatics, btx440, 10.1093/bioinformatics/btx440Published: 7 July 2017 Section: Original Paper -
Research Article 7 July 2017
The value of prior knowledge in machine learning of complex network systems
Bioinformatics, btx438, 10.1093/bioinformatics/btx438Published: 7 July 2017 Section: Original Paper -
Research Article 7 July 2017
A Novel Data Structure to Support Ultra-fast Taxonomic Classification of Metagenomic Sequences with k-mer Signatures
Bioinformatics, btx432, 10.1093/bioinformatics/btx432Published: 7 July 2017 Section: Original Paper -
Research Article 7 July 2017
DeepLoc: Prediction of protein subcellular localization using deep learning
José Juan Almagro Armenteros; Casper Kaae Sønderby; Søren Kaae Sønderby; Henrik Nielsen; Ole WintherBioinformatics, btx431, 10.1093/bioinformatics/btx431Published: 7 July 2017 Section: Original Paper -
Corrected Proof
Brief Report 7 July 2017
VCF-Explorer: filtering and analysing whole genome VCF files
Bioinformatics, btx422, 10.1093/bioinformatics/btx422Published: 7 July 2017 Section: APPLICATIONS NOTE -
Research Article 7 July 2017
A Nonparametric Significance Test for Sampled Networks
Bioinformatics, btx419, 10.1093/bioinformatics/btx419Published: 7 July 2017 Section: Original Paper -
Research Article 6 July 2017
Reactome enhanced pathway visualisation
Bioinformatics, btx441, 10.1093/bioinformatics/btx441Published: 6 July 2017 Section: Original Paper -
Research Article 6 July 2017
ISEScan: automated identification of Insertion Sequence Elements in prokaryotic genomes
Bioinformatics, btx433, 10.1093/bioinformatics/btx433Published: 6 July 2017 Section: Original Paper -
Brief Report 6 July 2017
AlloSigMA: Allosteric Signalling and Mutation Analysis server
Bioinformatics, btx430, 10.1093/bioinformatics/btx430Published: 6 July 2017 Section: APPLICATIONS NOTE -
Research Article 4 July 2017
Linking Metabolic Network Features to Phenotypes using Sparse Group Lasso
Bioinformatics, btx427, 10.1093/bioinformatics/btx427Published: 4 July 2017 Section: Original Paper -
Brief Report 4 July 2017
TITINdb - a Computational Tool to Assess Titin's Role as a Disease Gene
Bioinformatics, btx424, 10.1093/bioinformatics/btx424Published: 4 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Research Article 4 July 2017
pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R
Bioinformatics, btx413, 10.1093/bioinformatics/btx413Published: 4 July 2017 Section: Original Paper -
Corrected Proof
Correction 4 July 2017
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals
Bioinformatics, btx387, 10.1093/bioinformatics/btx387Published: 4 July 2017 Section: Corrigendum -
Corrected Proof
Brief Report 3 July 2017
ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data
Bioinformatics, btx393, 10.1093/bioinformatics/btx393Published: 3 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Research Article 3 July 2017
Quark enables semi-reference-based compression of RNA-seq data
Bioinformatics, btx428, 10.1093/bioinformatics/btx428Published: 3 July 2017 Section: Original Paper -
Brief Report 3 July 2017
ProtDec-LTR2.0: An improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank
Bioinformatics, btx429, 10.1093/bioinformatics/btx429Published: 3 July 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 29 June 2017
SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments
Bioinformatics, btx363, 10.1093/bioinformatics/btx363Published: 29 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 29 June 2017
modPhEA: model organism Phenotype Enrichment Analysis of eukaryotic gene sets
Bioinformatics, btx426, 10.1093/bioinformatics/btx426Published: 29 June 2017 Section: APPLICATIONS NOTE -
Brief Report 29 June 2017
CausalR - extracting mechanistic sense from genome scale data
Bioinformatics, btx425, 10.1093/bioinformatics/btx425Published: 29 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Research Article 29 June 2017
FALCON: a toolbox for the fast contextualization of logical networks
Bioinformatics, btx380, 10.1093/bioinformatics/btx380Published: 29 June 2017 Section: Original Paper -
Corrected Proof
Correction 28 June 2017
ALTRE: workflow for defining ALTered regulatory elements using chromatin accessibility data
Bioinformatics, btx386, 10.1093/bioinformatics/btx386Published: 28 June 2017 Section: Corrigendum -
Brief Report 28 June 2017
GPU-powered model analysis with PySB/cupSODA
Bioinformatics, btx420, 10.1093/bioinformatics/btx420Published: 28 June 2017 Section: APPLICATIONS NOTE -
Research Article 28 June 2017
Inferring transcriptional logic from multiple dynamic experiments
Bioinformatics, btx407, 10.1093/bioinformatics/btx407Published: 28 June 2017 Section: Original Paper -
Research Article 28 June 2017
SVM-dependent pairwise HMM: an application to Protein pairwise alignments
Bioinformatics, btx391, 10.1093/bioinformatics/btx391Published: 28 June 2017 Section: Original Paper -
Corrected Proof
Research Article 26 June 2017
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes
Bioinformatics, btx421, 10.1093/bioinformatics/btx421Published: 26 June 2017 Section: Original Paper -
Corrected Proof
Brief Report 26 June 2017
HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques
Bioinformatics, btx418, 10.1093/bioinformatics/btx418Published: 26 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Research Article 26 June 2017
SCooP: an accurate and fast predictor of protein stability curves as a function of temperature
Bioinformatics, btx417, 10.1093/bioinformatics/btx417Published: 26 June 2017 Section: Original Paper -
Research Article 26 June 2017
Forecasting residue-residue contact prediction accuracy
Bioinformatics, btx416, 10.1093/bioinformatics/btx416Published: 26 June 2017 Section: Original Paper -
Corrected Proof
Brief Report 26 June 2017
The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics
Bioinformatics, btx415, 10.1093/bioinformatics/btx415Published: 26 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Review Article 26 June 2017
Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning
Bioinformatics, btx414, 10.1093/bioinformatics/btx414Published: 26 June 2017 Section: Review -
Corrected Proof
Brief Report 26 June 2017
TSIS: an R package to infer alternative splicing isoform switches for time-series data
Bioinformatics, btx411, 10.1093/bioinformatics/btx411Published: 26 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Research Article 26 June 2017
Partitioned learning of deep Boltzmann machines for SNP data
Bioinformatics, btx408, 10.1093/bioinformatics/btx408Published: 26 June 2017 Section: Original Paper -
Corrected Proof
Research Article 24 June 2017
Identification of transcript regulatory patterns in cell differentiation
Bioinformatics, btx406, 10.1093/bioinformatics/btx406Published: 24 June 2017 Section: Original Paper -
Corrected Proof
Research Article 24 June 2017
A multi-scenario genome-wide medical population genetics simulation framework
Bioinformatics, btx369, 10.1093/bioinformatics/btx369Published: 24 June 2017 Section: Original Paper -
Corrected Proof
Brief Report 24 June 2017
Spliceman2: a computational web server that predicts defects in pre-mRNA splicing
Bioinformatics, btx343, 10.1093/bioinformatics/btx343Published: 24 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 24 June 2017
pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments
Bioinformatics, btx368, 10.1093/bioinformatics/btx368Published: 24 June 2017 Section: APPLICATIONS NOTE -
Research Article 23 June 2017
High-speed and high-ratio referential genome compression
Bioinformatics, btx412, 10.1093/bioinformatics/btx412Published: 23 June 2017 Section: Original Paper -
Corrected Proof
Research Article 23 June 2017
Panoptes: web-based exploration of large scale genome variation data
Bioinformatics, btx410, 10.1093/bioinformatics/btx410Published: 23 June 2017 Section: Original Paper -
Research Article 23 June 2017
TSGSIS: A High-dimensional Grouped Variable Selection Approach for Detection of Whole-genome SNP–SNP Interactions
Bioinformatics, btx409, 10.1093/bioinformatics/btx409Published: 23 June 2017 Section: Original Paper -
Brief Report 23 June 2017
Multimodal Mechanistic Signatures for Neurodegenerative Diseases (NeuroMMSig): a web server for mechanism enrichment
Daniel Domingo-Fernández; Alpha Tom Kodamullil; Anandhi Iyappan; Mufassra Naz; Mohammad Asif Emon ...Bioinformatics, btx399, 10.1093/bioinformatics/btx399Published: 23 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 22 June 2017
UpSetR: an R package for the visualization of intersecting sets and their properties
Bioinformatics, btx364, 10.1093/bioinformatics/btx364Published: 22 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 22 June 2017
GfaPy: a flexible and extensible software library for handling sequence graphs in Python
Bioinformatics, btx398, 10.1093/bioinformatics/btx398Published: 22 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Brief Report 20 June 2017
NucliTrack: an integrated nuclei tracking application
Bioinformatics, btx404, 10.1093/bioinformatics/btx404Published: 20 June 2017 Section: APPLICATIONS NOTE -
Corrected Proof
Research Article 19 June 2017
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data
Bioinformatics, btx402, 10.1093/bioinformatics/btx402Published: 19 June 2017 Section: Original Paper -
Corrected Proof
Research Article 19 June 2017
BPP: a sequence-based algorithm for branch point prediction
Bioinformatics, btx401, 10.1093/bioinformatics/btx401Published: 19 June 2017 Section: Original Paper -
Corrected Proof
Brief Report 19 June 2017
BioQueue: a novel pipeline framework to accelerate bioinformatics analysis
Bioinformatics, btx403, 10.1093/bioinformatics/btx403Published: 19 June 2017 Section: APPLICATIONS NOTE
