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Bioinformatics  
Volume 37 Issue 24
 
15 December 2021
 
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REVIEW
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization 
 
Yingying Yu; Wenjia He; Junru Jin; Guobao Xiao ; Lizhen Cui ...
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Founder reconstruction enables scalable and seamless pangenomic analysis border= 
 
Tuukka Norri; Bastien Cazaux; Saska Dönges; Daniel Valenzuela ; Veli Mäkinen
 
 
Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data 
 
Niko Popitsch; Sandra Preuner; Thomas Lion
 
 
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints border= 
 
Dhong-Gun Won; Dong-Wook Kim; Junwoo Woo ; Kyoungyeul Lee
 
 
CCIP: predicting CTCF-mediated chromatin loops with transitivity border= 
 
Weibing Wang; Lin Gao; Yusen Ye; Yong Gao
 
 
 
Accurate spliced alignment of long RNA sequencing reads border= 
 
Kristoffer Sahlin; Veli Mäkinen
 
 
Transformation and differential abundance analysis of microbiome data incorporating phylogeny 
 
Chao Zhou; Hongyu Zhao; Tao Wang
 
 
Nanopore base calling on the edge border= 
 
Peter Pere┼ííni; Vladimír Bo┼ża; Bro┼ła Brejová; Tomá┼í Vina┼Ö
 
 
 
SEQUENCE ANALYSIS
 
 
 
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein'protein interaction information border= 
 
Hangyuan Yang; Minghui Wang; Xia Liu ; Xing-Ming Zhao; Ao Li
 
 
Accurate large-scale phylogeny-aware alignment using BAli-Phy 
 
Maya Gupta; Paul Zaharias; Tandy Warnow
 
 
 
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides 
 
Wenjia He; Yu Wang; Lizhen Cui; Ran Su ; Leyi Wei
 
 
An astonishing wealth of new proteasome homologs border= 
 
Adrian C D Fuchs; Vikram Alva; Andrei N Lupas
 
 
 
PHYLOGENETICS
 
 
 
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data 
 
Haoyun Lei; E Michael Gertz; Alejandro A Schäffer; Xuecong Fu ; Yifeng Tao ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Phosphate binding sites prediction in phosphorylation-dependent protein'protein interactions 
 
Zheng-Chang Lu; Fan Jiang; Yun-Dong Wu
 
 
 
GENE EXPRESSION
 
 
 
Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE) 
 
Akila J Seneviratne; Sean Peters; David Clarke; Michael Dausmann ; Michael Hecker ...
 
 
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells border= 
 
Yixin Zhao; Noah Dukler; Gilad Barshad ; Shushan Toneyan; Charles G Danko ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants border= 
 
Shuang Song; Nayang Shan; Geng Wang ; Xiting Yan; Jun S Liu ...
 
 
LINADMIX: evaluating the effect of ancient admixture events on modern populations 
 
Lily Agranat-Tamir; Shamam Waldman; Naomi Rosen; Benjamin Yakir ; Shai Carmi ...
 
 
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl 
 
Benjamin B Chu; Eric M Sobel; Rory Wasiolek; Seyoon Ko ; Janet S Sinsheimer ...
 
 
CHIT: an allele-specific method for testing the association between molecular quantitative traits and phenotype'genotype interaction 
 
Qi Yan; Erick Forno; Juan C Celedón; Wei Chen ; Daniel E Weeks
 
 
 
SYSTEMS BIOLOGY
 
 
 
Transfer learning via multi-scale convolutional neural layers for human'virus protein'protein interaction prediction 
 
Xiaodi Yang; Shiping Yang; Xianyi Lian; Stefan Wuchty ; Ziding Zhang
 
 
Cancer subtype identification by consensus guided graph autoencoders 
 
Cheng Liang; Mingchao Shang; Jiawei Luo
 
 
GdClean: removal of Gadolinium contamination in mass cytometry data 
 
Junwei Liu; Lulu Liu; Saisi Qu; Tongtong Zhang ; Danyang Wang ...
 
 
BioERP: biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions 
 
Xiaoqi Wang; Yaning Yang; Kenli Li; Wentao Li ; Fei Li ...
 
 
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets 
 
D A Salazar; N Pr┼żulj; C F Valencia
 
 
 
DATA AND TEXT MINING
 
 
 
Stable Iterative Variable Selection border= 
 
Mehrad Mahmoudian; Mikko S Venäläinen; Riku Klén; Laura L Elo
 
 
DMIL-IsoFun: predicting isoform function using deep multi-instance learning 
 
Guoxian Yu; Guangjie Zhou; Xiangliang Zhang; Carlotta Domeniconi ; Maozu Guo
 
 
Organism-specific training improves performance of linear B-cell epitope prediction border= 
 
Jodie Ashford; João Reis-Cunha; Igor Lobo ; Francisco Lobo; Felipe Campelo
 
 
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug'target interactions border= 
 
Tilman Hinnerichs; Robert Hoehndorf
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Automatic improvement of deep learning-based cell segmentation in time-lapse microscopy by neural architecture search border= 
 
Yanming Zhu; Erik Meijering
 
 
spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos border= 
 
Wim Thiels; Bart Smeets; Maxim Cuvelier ; Francesca Caroti; Rob Jelier
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data border= 
 
Parker Knight; Marie-Pierre L Gauthier; Carolina E Pardo ; Russell P Darst; Kevin Kapadia ...
 
 
Unfazed: parent-of-origin detection for large and small de novo variants border= 
 
Jonathan R Belyeu; Thomas A Sasani; Brent S Pedersen ; Aaron R Quinlan
 
 
 
SEQUENCE ANALYSIS
 
 
 
RENANO: a REference-based compressor for NANOpore FASTQ files 
 
Guillermo Dufort y Álvarez; Gadiel Seroussi; Pablo Smircich; José Sotelo-Silveira ; Idoia Ochoa ...
 
 
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity 
 
Sebastiaan Valkiers; Max Van Houcke; Kris Laukens; Pieter Meysman
 
 
 
PHYLOGENETICS
 
 
 
SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction border= 
 
Andreas Rempel; Roland Wittler
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data border= 
 
Hamed Khakzad; Lotta Happonen; Johan Malmström ; Lars Malmström
 
 
VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures 
 
Kliment Olechnovi─Ź; ─'eslovas Venclovas
 
 
NaViA: a program for the visual analysis of complex mass spectra border= 
 
Daniel Quetschlich; Tim K Esser; Thomas D Newport; Francesco Fiorentino ; Denis Shutin ...
 
 
 
GENE EXPRESSION
 
 
 
AQUARIUM: accurate quantification of circular isoforms using model-based strategy 
 
Guoxia Wen; Musheng Li; Fuyu Li; Zengyan Yang ; Tong Zhou ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
fastsimcoal2: demographic inference under complex evolutionary scenarios border= 
 
Laurent Excoffier; Nina Marchi; David Alexander Marques ; Remi Matthey-Doret; Alexandre Gouy ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC'MS profiling datasets border= 
 
Arnaud M Wolfer; Gonçalo D S Correia; Caroline J Sands ; Stephane Camuzeaux; Ada H Y Yuen ...
 
 
PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX border= 
 
François Moreews; Hugo Simon; Anne Siegel ; Florence Gondret; Emmanuelle Becker
 
 
 
DATA AND TEXT MINING
 
 
 
The DNA methylation haplotype (mHap) format and mHapTools 
 
Zhiqiang Zhang; Yuhao Dan; Yaochen Xu; Jiarui Zhang ; Xiaoqi Zheng ...
 
 
DUI: the drug use insights web server 
 
Zachary Prince; Deeptanshu Jha; Rahul Singh
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
libOmexMeta: enabling semantic annotation of models to support FAIR principles 
 
Ciaran Welsh; David P Nickerson; Anand Rampadarath; Maxwell L Neal ; Herbert M Sauro ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax border= 
 
Benjamin Schmid; Philipp Tripal; Zoltán Winter ; Ralph Palmisano
 
 
 
CORRIGENDUM
 
 
 
Corrigendum to: LipidQuant 1.0: automated data processing in lipid class separation'mass spectrometry quantitative workflows 
 
Denise Wolrab; Eva Cífková; Pavel ─'á┼ł; Miroslav Lísa ; Ond┼Öej Peterka ...
 
 
 
ERRATUM
 
 
 
Erratum to: BAli-Phy version 3: model-based co-estimation of alignment and phylogeny 
 
Benjamin D Redelings
 
 
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