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Bioinformatics  
Volume 38 Issue 13
 
1 July 2022
 
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Original Papers
 
 
 
 
Genome analysis
 
 
 
ODGI: understanding pangenome graphs border= 
 
Andrea Guarracino; Simon Heumos; Sven Nahnsen; Pjotr Prins ; Erik Garrison
 
 
Assessing and assuring interoperability of a genomics file format border= 
 
Yi Nian Niu; Eric G Roberts; Danielle Denisko; Michael M Hoffman
 
 
Deep structure integrative representation of multi-omics data for cancer subtyping 
 
Bo Yang; Yan Yang; Xueping Su
 
 
 
Sequence analysis
 
 
 
SPRISS: approximating frequent k-mers by sampling reads, and applications border= 
 
Diego Santoro; Leonardo Pellegrina; Matteo Comin ; Fabio Vandin
 
 
Predicting protein'peptide binding residues via interpretable deep learning 
 
Ruheng Wang; Junru Jin; Quan Zou; Kenta Nakai ; Leyi Wei
 
 
 
ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data 
 
Martin M Femenias; Juan C Santos; Jack W Sites, Jr; Luciano J Avila ; Mariana Morando
 
 
 
Phylogenetics
 
 
 
Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance 
 
Nadia Tahiri; Bernard Fichet; Vladimir Makarenkov
 
 
 
Gene expression
 
 
 
scPreGAN, a deep generative model for predicting the response of single-cell expression to perturbation 
 
Xiajie Wei; Jiayi Dong; Fei Wang
 
 
 
Genetics and population analysis
 
 
 
An automated multi-modal graph-based pipeline for mouse genetic discovery 
 
Zhuoqing Fang; Gary Peltz
 
 
 
Systems biology
 
 
 
GLIDER: function prediction from GLIDE-based neighborhoods border= 
 
Kapil Devkota; Henri Schmidt; Matt Werenski; James M Murphy ; Mert Erden ...
 
 
 
PersonaDrive: a method for the identification and prioritization of personalized cancer drivers 
 
Cesim Erten; Aissa Houdjedj; Hilal Kazan; Ahmed Amine Taleb Bahmed
 
 
AutoDC: an automatic machine learning framework for disease classification 
 
Yang Bai; Yang Li; Yu Shen; Mingyu Yang ; Wentao Zhang ...
 
 
PeakBot: machine-learning-based chromatographic peak picking border= 
 
Christoph Bueschl; Maria Doppler; Elisabeth Varga; Bernhard Seidl ; Mira Flasch ...
 
 
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities 
 
Huaxu Yu; Tao Huan
 
 
 
Data and text mining
 
 
 
Powerful molecule generation with simple ConvNet 
 
Hongyang K Yu; Hongjiang C Yu
 
 
HelixADMET: a robust and endpoint extensible ADMET system incorporating self-supervised knowledge transfer 
 
Shanzhuo Zhang; Zhiyuan Yan; Yueyang Huang; Lihang Liu ; Donglong He ...
 
 
Conditional generative modeling for de novo protein design with hierarchical functions border= 
 
Tim Kucera; Matteo Togninalli; Laetitia Meng-Papaxanthos
 
 
 
Bioimage informatics
 
 
 
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks border= 
 
Philippe Weitz; Yinxi Wang; Kimmo Kartasalo ; Lars Egevad; Johan Lindberg ...
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
Examining clustered somatic mutations with SigProfilerClusters border= 
 
Erik N Bergstrom; Mousumy Kundu; Noura Tbeileh; Ludmil B Alexandrov
 
 
ScisorWiz: visualizing differential isoform expression in single-cell long-read data border= 
 
Alexander N Stein; Anoushka Joglekar; Chi-Lam Poon ; Hagen U Tilgner
 
 
 
Genetics and population analysis
 
 
 
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics border= 
 
Florian Privé
 
 
 
Systems biology
 
 
 
CeCaFLUX: the first web server for standardized and visual instationary 13C metabolic flux analysis 
 
Zhentao Liu; Zhengdong Zhang; Sheng Liang; Zhen Chen ; Xiaoyao Xie ...
 
 
 
Databases and ontologies
 
 
 
MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics 
 
Jonathan Strutz; Kevin M Shebek; Linda J Broadbelt; Keith E J Tyo
 
 
webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration 
 
Zilong Zhang; Feifei Cui; Wei Su; Lijun Dou ; Anqi Xu ...
 
 
 
Bioimage informatics
 
 
 
Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data border= 
 
Melissa Grant-Peters; Charlotte Rich-Griffin; Jonathan E Grant-Peters ; Gianfelice Cinque; Calliope A Dendrou
 
 
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