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Bioinformatics  
Volume 38 Issue 18
 
15 September 2022
 
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Original Papers
 
 
 
 
Genome analysis
 
 
 
 
LanceOtron: a deep learning peak caller for genome sequencing experiments border= 
 
Lance D Hentges; Martin J Sergeant; Christopher B Cole; Damien J Downes ; Jim R Hughes ...
 
 
 
Identification of bacteriophage genome sequences with representation learning border= 
 
Zeheng Bai ; Yao-zhong Zhang; Satoru Miyano; Rui Yamaguchi; Kosuke Fujimoto ...
 
 
 
Sequence analysis
 
 
 
 
An improved residual network using deep fusion for identifying RNA 5-methylcytosine sites 
 
Xinjie Li; Shengli Zhang; Hongyan Shi
 
 
 
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning border= 
 
Vlad-Rare┼č D─ân─âil─â; C─ât─âlin Buiu
 
 
 
MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis border= 
 
Jun-Jie Zheng ; Po-Wen Wang; Tzu-Wen Huang; Yao-Jong Yang; Hua-Sheng Chiu ...
 
 
 
 
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing border= 
 
Hana Rozho┼łová ; Daniel Danciu; Stefan Stark; Gunnar Rätsch; André Kahles ...
 
 
 
Structural bioinformatics
 
 
 
 
Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling 
 
Jimin Pei; Jing Zhang; Qian Cong
 
 
 
Best templates outperform homology models in predicting the impact of mutations on protein stability 
 
Marina A Pak; Dmitry N Ivankov
 
 
 
Gene expression
 
 
 
 
Detecting retinal neural and stromal cell classes and ganglion cell subtypes based on transcriptome data with deep transfer learning 
 
Yeganeh Madadi ; Jian Sun; Hao Chen; Robert Williams; Siamak Yousefi
 
 
 
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes border= 
 
Keita Iida; Jumpei Kondo; Johannes Nicolaus Wibisana; Masahiro Inoue ; Mariko Okada
 
 
 
 
 
Genetics and population analysis
 
 
 
 
Incorporating family disease history and controlling case'control imbalance for population-based genetic association studies border= 
 
Yongwen Zhuang; Brooke N Wolford; Kisung Nam ; Wenjian Bi; Wei Zhou ...
 
 
 
Systems biology
 
 
 
 
Identifying cellular cancer mechanisms through pathway-driven data integration border= 
 
Sam F L Windels; Noël Malod-Dognin; Nata┼ía Pr┼żulj
 
 
 
Quasi-Entropy Closure: a fast and reliable approach to close the moment equations of the Chemical Master Equation 
 
Vincent Wagner; Benjamin Castellaz; Marco Oesting; Nicole Radde
 
 
 
Overcoming selection bias in synthetic lethality prediction border= 
 
Colm Seale; Yasin Tepeli; Joana P Gonçalves
 
 
 
Data and text mining
 
 
 
 
BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task border= 
 
Maria Mahbub; Sudarshan Srinivasan; Edmon Begoli ; Gregory D Peterson
 
 
 
CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure 
 
Yuhao Chen; Yanshi Hu; Xiaotian Hu ; Cong Feng; Ming Chen
 
 
 
Multidrug representation learning based on pretraining model and molecular graph for drug interaction and combination prediction 
 
Shujie Ren; Liang Yu ; Lin Gao
 
 
 
Bioimage informatics
 
 
 
 
Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level border= 
 
Longjie Li ; Arun Mouli Kolinjivadi; Kok Haur Ong; David M Young; Gabriel Pik Liang Marini ...
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
PanTools v3: functional annotation, classification and phylogenomics border= 
 
Eef M Jonkheer; Dirk-Jan M van Workum; Siavash Sheikhizadeh Anari; Balázs Brankovics ; Jorn R de Haan ...
 
 
 
ShinySyn: a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data 
 
Zhixia Xiao; Hon-Ming Lam
 
 
 
ColocQuiaL: a QTL-GWAS colocalization pipeline border= 
 
Brian Y Chen; William P Bone; Kim Lorenz; Michael Levin ; Marylyn D Ritchie ...
 
 
 
PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes border= 
 
Alexis Dereeper ; Marilyne Summo; Damien F Meyer
 
 
 
DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference border= 
 
Vonn Walter ; Hyo Young Choi; Xiaobei Zhao; Yan Gao; Jeremiah Holt ...
 
 
 
Sequence analysis
 
 
 
 
SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants 
 
Gabriel Cia; Jean Marc Kwasigroch; Marianne Rooman; Fabrizio Pucci
 
 
 
ViReMaShiny: an interactive application for analysis of viral recombination data border= 
 
Jason Yeung; Andrew L Routh
 
 
 
The K-mer File Format: a standardized and compact disk representation of sets of k-mers border= 
 
Yoann Dufresne; Teo Lemane; Pierre Marijon; Pierre Peterlongo ; Amatur Rahman ...
 
 
 
Structural bioinformatics
 
 
 
 
ToxSTAR: drug-induced liver injury prediction tool for the web environment  
 
Hyun Kil Shin; Hang-Suk Chun; Sangwoo Lee ; Se-Myo Park; Daeui Park ...
 
 
 
MIB2: metal ion-binding site prediction and modeling server 
 
Chih-Hao Lu; Chih-Chieh Chen ; Chin-Sheng Yu; Yen-Yi Liu; Jia-Jun Liu ...
 
 
 
Gene expression
 
 
 
 
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments border= 
 
Federico Ansaloni; Nicolò Gualandi; Mauro Esposito ; Stefano Gustincich; Remo Sanges
 
 
 
Genetics and population analysis
 
 
 
 
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project 
 
Eric Ruan ; Erika Nemeth; Richard Moffitt; Lorena Sandoval; Mitchell J Machiela ...
 
 
 
Systems biology
 
 
 
 
NMRpQuant: an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles border=  
 
Panteleimon G Takis; Ivan Vuckovic; Tricia Tan; Aleksandar Denic; John C Lieske ...
 
 
 
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models 
 
Franco Pradelli; Giovanni Minervini ; Silvio C E Tosatto
 
 
 
Data and text mining
 
 
 
 
REALGAR: a web app of integrated respiratory omics data  
 
Mengyuan Kan; Avantika R Diwadkar; Supriya Saxena; Haoyue Shuai; Jaehyun Joo ...
 
 
 
BioCaster in 2021: automatic disease outbreaks detection from global news media border= 
 
Zaiqiao Meng ; Anya Okhmatovskaia; Maxime Polleri; Yannan Shen; Guido Powell ...
 
 
 
tmVar 3.0: an improved variant concept recognition and normalization tool border= 
 
Chih-Hsuan Wei; Alexis Allot; Kevin Riehle ; Aleksandar Milosavljevic; Zhiyong Lu
 
 
 
CPRiL: compound'protein relationships in literature 
 
Ammar Qaseem; Stefan Günther
 
 
 
Databases and ontologies
 
 
 
 
TargetMine 2022: a new vision into drug target analysis border= 
 
Yi-An Chen; Rodolfo S Allendes Osorio; Kenji Mizuguchi
 
 
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