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Bioinformatics  
Volume 38 Issue 15
 
1 August 2022
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors 
 
Lily Zheng; Noushin Niknafs; Laura D Wood; Rachel Karchin ; Robert B Scharpf
 
 
MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads 
 
Weizhi Song; Shan Zhang; Torsten Thomas
 
 
A rarefaction-without-resampling extension of PERMANOVA for testing presence'absence associations in the microbiome 
 
Yi-Juan Hu; Glen A Satten
 
 
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation border= 
 
P J Bradbury; T Casstevens; S E Jensen ; L C Johnson; Z R Miller ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
scCNC: a method based on capsule network for clustering scRNA-seq data 
 
Hai-Yun Wang; Jian-Ping Zhao; Chun-Hou Zheng; Yan-Sen Su
 
 
 
Shepherd: accurate clustering for correcting DNA barcode errors border= 
 
Nik Tavakolian; João Guilherme Frazão; Devin Bendixsen; Rike Stelkens ; Chun-Biu Li
 
 
Figbird: a probabilistic method for filling gaps in genome assemblies 
 
Sumit Tarafder; Mazharul Islam; Swakkhar Shatabda; Atif Rahman
 
 
 
PHYLOGENETICS
 
 
 
NetRAX: accurate and fast maximum likelihood phylogenetic network inference border= 
 
Sarah Lutteropp; Céline Scornavacca; Alexey M Kozlov; Benoit Morel ; Alexandros Stamatakis
 
 
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2 border= 
 
Cheng Ye; Bryan Thornlow; Angie Hinrichs ; Alexander Kramer; Cade Mirchandani ...
 
 
 
GENE EXPRESSION
 
 
 
NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing border= 
 
Yupei You; Michael B Clark; Heejung Shim
 
 
 
Identifying interactions in omics data for clinical biomarker discovery using symbolic regression border= 
 
Niels Johan Christensen; Samuel Demharter; Meera Machado ; Lykke Pedersen; Marco Salvatore ...
 
 
Batch alignment via retention orders for preprocessing large-scale multi-batch LC-MS experiments 
 
František Malinka; Ashkan Zareie; Jan Prochazka; Radislav Sedlacek ; Vendula Novosadova
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes border= 
 
Yilei Huang; Harald Ringbauer
 
 
XSI'a genotype compression tool for compressive genomics in large biobanks border= 
 
Rick Wertenbroek; Simone Rubinacci; Ioannis Xenarios; Yann Thoma ; Olivier Delaneau
 
 
 
SYSTEMS BIOLOGY
 
 
 
Functional characterization of co-phosphorylation networks 
 
Marzieh Ayati; Serhan Yılmaz; Mark R Chance; Mehmet Koyuturk
 
 
 
DATA AND TEXT MINING
 
 
 
Sequence tagging for biomedical extractive question answering border= 
 
Wonjin Yoon; Richard Jackson; Aron Lagerberg; Jaewoo Kang
 
 
Robust identification of temporal biomarkers in longitudinal omics studies border= 
 
Ahmed A Metwally; Tom Zhang; Si Wu; Ryan Kellogg ; Wenyu Zhou ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences border= 
 
Pavel Vazquez; Kayoko Hirayama-Shoji; Steffen Novik ; Stefan Krauss; Simon Rayner
 
 
 
BIOIMAGE INFORMATICS
 
 
 
MIAMI: mutual information-based analysis of multiplex imaging data border= 
 
Souvik Seal; Debashis Ghosh
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
SPEAR: Systematic ProtEin AnnotatoR border= 
 
Matthew Crown; Natália Teruel; Rafael Najmanovich; Matthew Bashton
 
 
 
SEQUENCE ANALYSIS
 
 
 
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data 
 
Piyush Ranjan; Christopher A Brown; John R Erb-Downward; Robert P Dickson
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
MetBP: a software tool for detection of interaction between metal ion'RNA base pairs 
 
Parthajit Roy; Dhananjay Bhattacharyya
 
 
DrawTetrado to create layer diagrams of G4 structures border= 
 
Michal Zurkowski; Tomasz Zok; Marta Szachniuk
 
 
PrISM: precision for integrative structural models 
 
Varun Ullanat; Nikhil Kasukurthi; Shruthi Viswanath
 
 
 
GENE EXPRESSION
 
 
 
riboCleaner: a pipeline to identify and quantify rRNA read contamination from RNA-seq data in plants 
 
Pu Huang; Erin Davis; Xia Cao; Hunter J Cameron
 
 
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2 border= 
 
Emil K Gustavsson; David Zhang; Regina H Reynolds ; Sonia Garcia-Ruiz; Mina Ryten
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR metabolomics data border= 
 
D Bizzarri; M J T Reinders; M Beekman ; P E Slagboom; E B van den Akker
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Integrative data semantics through a model-enabled data stewardship border= 
 
Philipp Wegner; Sebastian Schaaf; Mischa Uebachs; Daniel Domingo-Fernández ; Yasamin Salimi ...
 
 
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