Bittrich, Sebastian Rose, Yana Segura, Joan Lowe, Robert Westbrook, John D Duarte, Jose M Burley, Stephen K
Published in
Bioinformatics (Oxford, England)
Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a tr...
McHale, Peter Quinlan, Aaron R
Published in
Bioinformatics (Oxford, England)
We present trfermikit, a software tool designed to detect deletions larger than 50 bp occurring in Variable Number Tandem Repeats (VNTRs) using Illumina DNA sequencing reads. In such regions, it achieves a better trade-off between sensitivity and false discovery than a state-of-the-art structural variation (SV) caller, Manta, and complements it by ...
Gu, Zuguang Hübschmann, Daniel
Published in
Bioinformatics (Oxford, England)
Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In this work, we introduce a new R package InteractiveComplexHeatmap that brings interactivity to the widely used ComplexHeatmap package. InteractiveComplexHeatmap is designed with an easy-to-use interface where static comple...
Buterez, David Bica, Ioana Tariq, Ifrah Andrés-Terré, Helena Liò, Pietro
Published in
Bioinformatics (Oxford, England)
Single-cell RNA sequencing allows high-resolution views of individual cells for libraries of up to millions of samples, thus motivating the use of deep learning for analysis. In this study, we introduce the use of graph neural networks for the unsupervised exploration of scRNA-seq data by developing a variational graph autoencoder architecture with...
Chaguza, Chrispin Tonkin-Hill, Gerry Lo, Stephanie W Hadfield, James Croucher, Nicholas J Harris, Simon R Bentley, Stephen D
Published in
Bioinformatics (Oxford, England)
Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, which increases genomic sequence diversity and can facilitate adaptation. Several methods and tools have been developed to detect genomic regions recently affected by recombination. Exploration and visualisation of such recombination events can reveal v...
Yang, Xiaodi Yang, Shiping Lian, Xianyi Wuchty, Stefan Zhang, Ziding
Published in
Bioinformatics (Oxford, England)
To complement experimental efforts, machine learning-based computational methods are playing an increasingly important role to predict human-virus protein-protein interactions (PPIs). Furthermore, transfer learning can effectively apply prior knowledge obtained from a large source dataset/task to a small target dataset/task, improving prediction pe...
Thumuluri, Vineet Martiny, Hannah-Marie Armenteros, Jose J Almagro Salomon, Jesper Nielsen, Henrik Johansen, Alexander R
Published in
Bioinformatics (Oxford, England)
Solubility and expression levels of proteins can be a limiting factor for large-scale studies and industrial production. By determining the solubility and expression directly from the protein sequence, the success rate of wet-lab experiments can be increased. In this study, we focus on predicting the solubility and usability for purification of pro...
Ju, Fusong Zhu, Jianwei Zhang, Qi Wei, Guozheng Sun, Shiwei Zheng, Wei-Mou Bu, Dongbo
Published in
Bioinformatics (Oxford, England)
Accurate prediction of protein structure relies heavily on exploiting multiple sequence alignment (MSA) for residue mutations and correlations as this information specifies protein tertiary structure. The widely-used prediction approaches usually transform MSA into inter-mediate models, say position-specific scoring matrix or profile hidden Markov ...
Tang, Deyou Li, Yuchen Tan, Daqiang Fu, Juan Tang, Yelei Lin, Jiabin Zhao, Rong Du, Hongli Zhao, Zhongming
Published in
Bioinformatics (Oxford, England)
The k-mer frequency in whole genome sequences provides researchers with an insightful perspective on genomic complexity, comparative genomics, metagenomics, and phylogeny. The current k-mer counting tools are typically slow, and they require large memory and hard disk for assembled genome analysis. We propose a novel and ultra-fast k-mer counting a...
Khatiwada, Aastha Wolf, Bethany J Yilmaz, Ayse Selen Ramos, Paula S Pietrzak, Maciej Lawson, Andrew Hunt, Kelly J Kim, Hang J Chung, Dongjun
Published in
Bioinformatics (Oxford, England)
In spite of great success of genome-wide association studies (GWAS), multiple challenges still remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), each with small or moderate effect sizes. Second, our understanding of the functional mechanisms through which genetic variants are associated with comple...
