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The Journal Citation ReportsTM, from Clarivate, 2022 have been released and we are delighted to share the latest Impact Factor for Briefings in Bioinformatics has increased to 13.994. Congratulations and appreciation to the high standards and work of our authors, editors, reviewers and readers. Celebrate with us by enjoying a curated collection of the most impactful articles from Briefings in Bioinformatics over the past two years - read them here.
 
 
 
 
 
 
Briefings in Bioinformatics  
Volume 23 Issue 4
 
July 2022
 
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Articles
 
 
 
Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation 
 
Weikang Gong; JunJie Wee; Min-Chun Wu; Xiaohan Sun ; Chunhua Li ...
 
 
circRIP: an accurate tool for identifying circRNA'RBP interactions 
 
Xin Dong; Ke Chen; Wenbo Chen; Jun Wang ; Liuping Chang ...
 
 
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs border= 
 
Neeladri Sen; Ivan Anishchenko; Nicola Bordin ; Ian Sillitoe; Sameer Velankar ...
 
 
A heterogeneous network-based method with attentive meta-path extraction for predicting drug'target interactions 
 
Hongzhun Wang; Feng Huang; Zhankun Xiong; Wen Zhang
 
 
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins border= 
 
Xinxin Peng; Xiaoyu Wang; Yuming Guo ; Zongyuan Ge; Fuyi Li ...
 
 
 
KLFDAPC: a supervised machine learning approach for spatial genetic structure analysis border= 
 
Xinghu Qin; Charleston W K Chiang; Oscar E Gaggiotti
 
 
Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2 
 
Yunda Si; Chengfei Yan
 
 
Exploring the kinase-inhibitor fragment interaction space facilitates the discovery of kinase inhibitor overcoming resistance by mutations 
 
Zhi-Zheng Wang; Ming-Shu Wang; Fan Wang; Xing-Xing Shi ; Wei Huang ...
 
 
BETA: a comprehensive benchmark for computational drug'target prediction border= 
 
Nansu Zong; Ning Li; Andrew Wen; Victoria Ngo ; Yue Yu ...
 
 
A computational framework to unify orthogonal information in DNA methylation and copy number aberrations in cell-free DNA for early cancer detection 
 
Qiang Wei; Chao Jin; Yang Wang; Shanshan Guo ; Xu Guo ...
 
 
 
A penalized linear mixed model with generalized method of moments for prediction analysis on high-dimensional multi-omics data 
 
Xiaqiong Wang; Yalu Wen
 
 
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning 
 
Anthony Huffman; Edison Ong; Junguk Hur; Adonis D'Mello ; Hervé Tettelin ...
 
 
The prediction approach of drug-induced liver injury: response to the issues of reproducible science of artificial intelligence in real-world applications 
 
Zhao Chen; Yin Jiang; Xiaoyu Zhang; Rui Zheng ; Ruijin Qiu ...
 
 
DeepSCP: utilizing deep learning to boost single-cell proteome coverage 
 
Bing Wang; Yue Wang; Yu Chen; Mengmeng Gao ; Jie Ren ...
 
 
Structural landscapes of PPI interfaces 
 
Carlos H M Rodrigues; Douglas E V Pires; Tom L Blundell; David B Ascher
 
 
Quantitative estimation of intracellular oxidative stress in human tissues border= 
 
Jun Bai; Renbo Tan; Zheng An; Ying Xu
 
 
HDIContact: a novel predictor of residue'residue contacts on hetero-dimer interfaces via sequential information and transfer learning strategy 
 
Wei Zhang; Qiaozhen Meng; Jianxin Wang; Fei Guo
 
 
PIWI-interacting RNAs in human diseases: databases and computational models 
 
Tianjiao Zhang; Liang Chen; Rongzhen Li; Ning Liu ; Xiaobing Huang ...
 
 
STNN-DDI: a Substructure-aware Tensor Neural Network to predict Drug'Drug Interactions 
 
Hui Yu; ShiYu Zhao; JianYu Shi
 
 
ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data 
 
Ho-Jin Gwak; Mina Rho
 
 
Evaluation of propensity score methods for causal inference with high-dimensional covariates 
 
Qian Gao; Yu Zhang; Hongwei Sun; Tong Wang
 
 
ggmsa: a visual exploration tool for multiple sequence alignment and associated data 
 
Lang Zhou; Tingze Feng; Shuangbin Xu; Fangluan Gao ; Tommy T Lam ...
 
 
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology border= 
 
Anna Niarakis; Dagmar Waltemath; James Glazier ; Falk Schreiber; Sarah M Keating ...
 
 
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks border= 
 
Polina Suter; Jack Kuipers; Niko Beerenwinkel
 
 
idenMD-NRF: a ranking framework for miRNA-disease association identification 
 
Wenxiang Zhang; Hang Wei; Bin Liu
 
 
Heterogeneous data integration methods for patient similarity networks border= 
 
Jessica Gliozzo; Marco Mesiti; Marco Notaro; Alessandro Petrini ; Alex Patak ...
 
 
DSEATM: drug set enrichment analysis uncovering disease mechanisms by biomedical text mining 
 
Zhi-Hui Luo; Li-Da Zhu; Ya-Min Wang; Sheng Hu Qian ; Menglu Li ...
 
 
Disease spreading modeling and analysis: a survey 
 
Pietro Hiram Guzzi; Francesco Petrizzelli; Tommaso Mazza
 
 
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches 
 
L A Bugnon; A A Edera; S Prochetto; M Gerard ; J Raad ...
 
 
Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames border= 
 
Mengyun Jiang; Weidong Ning; Shishi Wu ; Xingwei Wang; Kun Zhu ...
 
 
Multiphysical graph neural network (MP-GNN) for COVID-19 drug design 
 
Xiao-Shuang Li; Xiang Liu; Le Lu; Xian-Sheng Hua ; Ying Chi ...
 
 
Entropy-based inference of transition states and cellular trajectory for single-cell transcriptomics 
 
Yanglan Gan; Cheng Guo; Wenjing Guo; Guangwei Xu ; Guobing Zou
 
 
ELSSI: parallel SNP'SNP interactions detection by ensemble multi-type detectors 
 
Xin Wang; Xia Cao; Yuantao Feng; Maozu Guo ; Guoxian Yu ...
 
 
Network approaches for modeling the effect of drugs and diseases border= 
 
T J Rintala; Arindam Ghosh; V Fortino
 
 
BayeshERG: a robust, reliable and interpretable deep learning model for predicting hERG channel blockers 
 
Hyunho Kim; Minsu Park; Ingoo Lee; Hojung Nam
 
 
iDRNA-ITF: identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework 
 
Ning Wang; Ke Yan; Jun Zhang; Bin Liu
 
 
DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data 
 
Matthew Karikomi; Peijie Zhou; Qing Nie
 
 
PRES: a webserver for decoding the functional perturbations of RNA editing sites 
 
Dezhong Lv; Kang Xu; Changbo Yang; Yujie Liu ; Ya Luo ...
 
 
PCfun: a hybrid computational framework for systematic characterization of protein complex function 
 
Varun S Sharma; Andrea Fossati; Rodolfo Ciuffa; Marija Buljan ; Evan G Williams ...
 
 
Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction 
 
Boris Vishnepolsky; Maya Grigolava; Grigol Managadze; Andrei Gabrielian ; Alex Rosenthal ...
 
 
Evaluating hierarchical machine learning approaches to classify biological databases 
 
Pâmela M Rezende; Joicymara S Xavier; David B Ascher; Gabriel R Fernandes ; Douglas E V Pires
 
 
Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components 
 
Haiping Zhang; Konda Mani Saravanan; Yang Yang; Yanjie Wei ; Pan Yi ...
 
 
Deepening the knowledge of rare diseases dependent on angiogenesis through semantic similarity clustering and network analysis border= 
 
Raquel Pagano-Márquez; José Córdoba-Caballero; Beatriz Martínez-Poveda ; Ana R Quesada; Elena Rojano ...
 
 
Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST 
 
Klaudia Adamowicz; Andreas Maier; Jan Baumbach; David B Blumenthal
 
 
Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for Plasmodium proteins 
 
Priya Gupta; Sureshkumar Venkadesan; Debasisa Mohanty
 
 
A comprehensive comparison on cell-type composition inference for spatial transcriptomics data 
 
Jiawen Chen; Weifang Liu; Tianyou Luo; Zhentao Yu ; Minzhi Jiang ...
 
 
Virus finding tools: current solutions and limitations 
 
Grete Francesca Privitera; Salvatore Alaimo; Alfredo Ferro; Alfredo Pulvirenti
 
 
TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach 
 
Wenjuan Nie; Lei Deng
 
 
Cell'cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies 
 
Lihong Peng; Feixiang Wang; Zhao Wang; Jingwei Tan ; Li Huang ...
 
 
TACOS: a novel approach for accurate prediction of cell-specific long noncoding RNAs subcellular localization border= 
 
Young-Jun Jeon; Md Mehedi Hasan; Hyun Woo Park ; Ki Wook Lee; Balachandran Manavalan
 
 
BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria border= 
 
Robson P Bonidia; Anderson P Avila Santos; Breno L S de Almeida ; Peter F Stadler; Ulisses N da Rocha ...
 
 
A comprehensive benchmarking of WGS-based deletion structural variant callers 
 
Varuni Sarwal; Sebastian Niehus; Ram Ayyala; Minyoung Kim ; Aditya Sarkar ...
 
 
Best practice and reproducible science are required to advance artificial intelligence in real-world applications 
 
Zhichao Liu; Ting Li; Skylar Connor; Shraddha Thakkar ; Ruth Roberts ...
 
 
Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks 
 
Emilio Fenoy; Alejando A Edera; Georgina Stegmayer
 
 
ConSIG: consistent discovery of molecular signature from OMIC data 
 
Fengcheng Li; Jiayi Yin; Mingkun Lu; Qingxia Yang ; Zhenyu Zeng ...
 
 
Multi-omics to characterize the functional relationships of R-loops with epigenetic modifications, RNAPII transcription and gene expression 
 
Xingxin Pan; L Frank Huang
 
 
Accurate identification of bacteriophages from metagenomic data using Transformer border= 
 
Jiayu Shang; Xubo Tang; Ruocheng Guo ; Yanni Sun
 
 
PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data 
 
Mengfei Liu; Linlin Hao; Sien Yang; Xiaohui Wu
 
 
Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs 
 
Madhu Sharma; Indra Prakash Jha; Smriti Chawla; Neetesh Pandey ; Omkar Chandra ...
 
 
iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model 
 
Hiroyuki Kurata; Sho Tsukiyama; Balachandran Manavalan
 
 
LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays 
 
Dat Thanh Nguyen; Quan Hoang Nguyen; Nguyen Thuy Duong; Nam S Vo
 
 
MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network 
 
Guiying Dong; Zi-Chao Zhang; Jianfeng Feng; Xing-Ming Zhao
 
 
Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine border= 
 
Ryuji Hamamoto; Ken Takasawa; Hidenori Machino ; Kazuma Kobayashi; Satoshi Takahashi ...
 
 
Mitigating cold-start problems in drug-target affinity prediction with interaction knowledge transferring 
 
Tri Minh Nguyen; Thin Nguyen; Truyen Tran
 
 
Deep generative model for therapeutic targets using transcriptomic disease-associated data'USP7 case study 
 
Tiago Pereira; Maryam Abbasi; Rita I Oliveira; Romina A Guedes ; Jorge A R Salvador ...
 
 
Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization 
 
Jianfeng Li; Benben Miao; Shixiang Wang; Wei Dong ; Houshi Xu ...
 
 
Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes border= 
 
Yunhee Jeong; Lisa Barros de Andrade e Sousa; Dominik Thalmeier ; Reka Toth; Marlene Ganslmeier ...
 
 
Bioinformatics strategies for studying the molecular mechanisms of fungal extracellular vesicles with a focus on infection and immune responses 
 
Kandasamy Saravanakumar; Sugavaneswaran Siva Santosh; MohamedAli Afaan Ahamed; Anbazhagan Sathiyaseelan ; Ghazala Sultan ...
 
 
A comprehensive analysis of the IEDB MHC class-I automated benchmark 
 
Raphael Trevizani; Zhen Yan; Jason A Greenbaum; Alessandro Sette ; Morten Nielsen ...
 
 
Evaluation of different computational methods for DNA methylation-based biological age 
 
Pietro Di Lena; Claudia Sala; Christine Nardini
 
 
BatchDTA: implicit batch alignment enhances deep learning-based drug'target affinity estimation 
 
Hongyu Luo; Yingfei Xiang; Xiaomin Fang; Wei Lin ; Fan Wang ...
 
 
FL-DTD: an integrated pipeline to predict the drug interacting targets by feedback loop-based network analysis 
 
Dong Lu; Rongrong Pan; Wenxuan Wu; Yanyan Zhang ; Shensuo Li ...
 
 
Resolving single-cell copy number profiling for large datasets 
 
Wang Ruohan; Zhang Yuwei; Wang Mengbo; Feng Xikang ; Wang Jianping ...
 
 
Adaptive sequencing using nanopores and deep learning of mitochondrial DNA 
 
Artem Danilevsky; Avital Luba Polsky; Noam Shomron
 
 
Response to ˜Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression based clustering', Zhang et al. 
 
Wennan Chang; Chi Zhang; Sha Cao
 
 
Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA 
 
Xianglin Zhang; Xiaodong Jia; Bixi Zhong; Lei Wei ; Jiaqi Li ...
 
 
SYSMut: decoding the functional significance of rare somatic mutations in cancer 
 
Sirvan Khalighi; Peronne Joseph; Deepak Babu; Salendra Singh ; Thomas LaFramboise ...
 
 
High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands 
 
Tong Yang; Feng Gao
 
 
AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification border= 
 
Mehdi Yazdani-Jahromi; Niloofar Yousefi; Aida Tayebi ; Elayaraja Kolanthai; Craig J Neal ...
 
 
A deep learning method for predicting metabolite'disease associations via graph neural network 
 
Feiyue Sun; Jianqiang Sun; Qi Zhao
 
 
PSnoD: identifying potential snoRNA-disease associations based on bounded nuclear norm regularization 
 
Zijie Sun; Qinlai Huang; Yuhe Yang; Shihao Li ; Hao Lv ...
 
 
Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference border= 
 
Daniel N Sosa; Russ B Altman
 
 
Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis 
 
Xinyi Xu; Xiaokang Yu; Gang Hu; Kui Wang ; Jingxiao Zhang ...
 
 
Statistical challenges in longitudinal microbiome data analysis border= 
 
Saritha Kodikara; Susan Ellul; Kim-Anh Lê Cao
 
 
Prediction of allosteric druggable pockets of cyclin-dependent kinases 
 
Shangbo Ning; Huiwen Wang; Chen Zeng; Yunjie Zhao
 
 
De novo molecular design with deep molecular generative models for PPI inhibitors 
 
Jianmin Wang; Yanyi Chu; Jiashun Mao; Hyeon-Nae Jeon ; Haiyan Jin ...
 
 
Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery border= 
 
Wiktoria Wilman; Sonia Wróbel; Weronika Bielska ; Piotr Deszynski; PaweÅ‚ Dudzic ...
 
 
m6  Aexpress-BHM: predicting m6A regulation of gene expression in multiple-groups context by a Bayesian hierarchical mixture model 
 
Teng Zhang; Shao-wu Zhang; Jian Feng; Bei Zhang
 
 
CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences 
 
Zhe Zhang; Miaomiao Zhu; Qi Xie; Robert M Larkin ; Xueping Shi ...
 
 
Immune infiltration and clinical significance analyses of the coagulation-related genes in hepatocellular carcinoma 
 
Qifan He; Jian Yang; Yonghai Jin
 
 
Chinese medical dialogue information extraction via contrastive multi-utterance inference 
 
Jianhua Dai; Chao Jiang; Ruoyao Peng; Daojian Zeng ; Yangding Li
 
 
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