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Highly Cited Articles from Briefings in Bioinformatics
 
Discover a new collection from Briefings in Bioinformatics, featuring the 20 most-cited articles from 2019 and 2020. These articles showcase the impact that the journal has on life sciences and provide a sample of the quality research that the journal has to offer.
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Briefings in Bioinformatics  
Volume 22 Issue 6
 
November 2021
 
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Articles
 
 
 
Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19 border= 
 
Marios Tomazou; Marilena M Bourdakou; George Minadakis ; Margarita Zachariou; Anastasis Oulas ...
 
 
DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity border= 
 
Guangyuan Li; Balaji Iyer; V B Surya Prasath ; Yizhao Ni; Nathan Salomonis
 
 
MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph 
 
Yanyi Chu; Xuhong Wang; Qiuying Dai; Yanjing Wang ; Qiankun Wang ...
 
 
MMFGRN: a multi-source multi-model fusion method for gene regulatory network reconstruction 
 
Wenying He; Jijun Tang; Quan Zou; Fei Guo
 
 
An effective self-supervised framework for learning expressive molecular global representations to drug discovery 
 
Pengyong Li; Jun Wang; Yixuan Qiao; Hao Chen ; Yihuan Yu ...
 
 
 
Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors 
 
Yue Zhao; Xiang-Gui Wang; Zhong-Ye Ma; Guo-Li Xiong ; Zhi-Jiang Yang ...
 
 
Forman persistent Ricci curvature (FPRC)-based machine learning models for protein'ligand binding affinity prediction 
 
JunJie Wee; Kelin Xia
 
 
Improving Single-Cell RNA-seq Clustering by Integrating Pathways 
 
Chenxing Zhang; Lin Gao; Bingbo Wang; Yong Gao
 
 
NSL2CD: identifying potential circRNA'disease associations based on network embedding and subspace learning 
 
Qiu Xiao; Yu Fu; Yide Yang; Jianhua Dai ; Jiawei Luo
 
 
SSI'DDI: substructure'substructure interactions for drug'drug interaction prediction 
 
Arnold K Nyamabo; Hui Yu; Jian-Yu Shi
 
 
 
MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction 
 
Xiao-Chen Zhang; Cheng-Kun Wu; Zhi-Jiang Yang; Zhen-Xing Wu ; Jia-Cai Yi ...
 
 
Resilience function uncovers the critical transitions in cancer initiation 
 
Yan Li; Shao-Wu Zhang
 
 
Prediction of tumor purity from gene expression data using machine learning 
 
Bonil Koo; Je-Keun Rhee
 
 
EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps border= 
 
Jiahua He; Sheng-You Huang
 
 
Updates to HCOP: the HGNC comparison of orthology predictions tool border= 
 
Bethan Yates; Kristian A Gray; Tamsin E M Jones; Elspeth A Bruford
 
 
Comparison of sparse biclustering algorithms for gene expression datasets border= 
 
Kath Nicholls; Chris Wallace
 
 
The peripheral and core regions of virus-host network of COVID-19 
 
Bingbo Wang; Xianan Dong; Jie Hu; Xiujuan Ma ; Chao Han ...
 
 
Exploring effectiveness of ab-initio protein'protein docking methods on a novel antibacterial protein complex dataset 
 
Wei Zhang; Qiaozhen Meng; Jijun Tang; Fei Guo
 
 
Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision border= 
 
Philip Davies; Matt Jones; Juntai Liu ; Daniel Hebenstreit
 
 
A novel computational framework for genome-scale alternative transcription units prediction 
 
Qi Wang; Zhaoqian Liu; Bo Yan; Wen-Chi Chou ; Laurence Ettwiller ...
 
 
Multi-view Multichannel Attention Graph Convolutional Network for miRNA'disease association prediction 
 
Xinru Tang; Jiawei Luo; Cong Shen; Zihan Lai
 
 
KCRR: a nonlinear machine learning with a modified genomic similarity matrix improved the genomic prediction efficiency 
 
Bingxing An; Mang Liang; Tianpeng Chang; Xinghai Duan ; Lili Du ...
 
 
StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides 
 
Phasit Charoenkwan; Wararat Chiangjong; Chanin Nantasenamat; Md Mehedi Hasan ; Balachandran Manavalan ...
 
 
ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes 
 
Shuhui Liu; Yupei Zhang; Xuequn Shang; Zhaolei Zhang
 
 
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches border= 
 
Anna Onisiforou; George M Spyrou
 
 
Knowledge bases and software support for variant interpretation in precision oncology border= 
 
Florian Borchert; Andreas Mock; Aurelie Tomczak ; Jonas Hügel; Samer Alkarkoukly ...
 
 
Pan-cancer application of a lung-adenocarcinoma-derived gene-expression-based prognostic predictor border= 
 
Deborah F Nacer; Helena Liljedahl; Anna Karlsson ; David Lindgren; Johan Staaf
 
 
Identification of multiple RNAs using feature fusion 
 
Dalwinder Singh; Akansha Madhawan; Joy Roy
 
 
Integration and interplay of machine learning and bioinformatics approach to identify genetic interaction related to ovarian cancer chemoresistance 
 
Kexin Chen; Haoming Xu; Yiming Lei; Pietro Lio ; Yuan Li ...
 
 
Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease 
 
Linhui Xie; Bing He; Pradeep Varathan; Kwangsik Nho ; Shannon L Risacher ...
 
 
WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values 
 
Le Ou-Yang; Dehan Cai; Xiao-Fei Zhang; Hong Yan
 
 
NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning 
 
Md Mehedi Hasan; Md Ashad Alam; Watshara Shoombuatong; Hong-Wen Deng ; Balachandran Manavalan ...
 
 
A new thinking: extended application of genomic selection to screen multiomics data for development of novel hypoxia-immune biomarkers and target therapy of clear cell renal cell carcinoma 
 
Cheng-Peng Gui; Jin-Huan Wei; Yu-Hang Chen; Liang-Min Fu ; Yi-Ming Tang ...
 
 
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure border= 
 
Yumei Li; Qing Sunny Shen; Qi Peng ; Wanqiu Ding; Jie Zhang ...
 
 
Network-based identification of key master regulators associated with an immune-silent cancer phenotype border= 
 
Raghvendra Mall; Mohamad Saad; Jessica Roelands ; Darawan Rinchai; Khalid Kunji ...
 
 
MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models 
 
Carlos A Ortiz-Mahecha; William A Agudelo; Manuel A Patarroyo; Manuel E Patarroyo ; Carlos F Suárez
 
 
A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics 
 
Christoph A Krettler; Gerhard G Thallinger
 
 
Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders 
 
Md Asif Nashiry; Shauli Sarmin Sumi; Mohammad Umer Sharif Shohan; Salem A Alyami ; A K M Azad ...
 
 
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries 
 
Yosef Masoudi-Sobhanzadeh; Aysan Salemi; Mohammad M Pourseif; Behzad Jafari ; Yadollah Omidi ...
 
 
ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome 
 
Bowen Song; Kunqi Chen; Yujiao Tang; Zhen Wei ; Jionglong Su ...
 
 
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning 
 
Yong-Zi Chen; Zhuo-Zhi Wang; Yanan Wang; Guoguang Ying ; Zhen Chen ...
 
 
Characterization and comparison of gene-centered human interactomes border= 
 
Ettore Mosca; Matteo Bersanelli; Tommaso Matteuzzi; Noemi Di Nanni ; Gastone Castellani ...
 
 
Reconciling multiple connectivity scores for drug repurposing border= 
 
Kewalin Samart; Phoebe Tuyishime; Arjun Krishnan; Janani Ravi
 
 
Utilizing graph machine learning within drug discovery and development border= 
 
Thomas Gaudelet; Ben Day; Arian R Jamasb; Jyothish Soman ; Cristian Regep ...
 
 
ARAMIS: From systematic errors of NGS long reads to accurate assemblies border= 
 
E Sacristán-Horcajada; S González-de la Fuente; R Peiró-Pastor; F Carrasco-Ramiro ; R Amils ...
 
 
Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data border= 
 
Jingzhe Lu; Xu Wang; Keyong Sun ; Xun Lan
 
 
Identification of genetic variations associated with drug resistance in non-small cell lung cancer patients undergoing systemic treatment border= 
 
Ruihan Luo; Chuang Ge; Xiao Xiao ; Jing Song; Shiqi Miao ...
 
 
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor 
 
Yuzhao Zhang; Xibing He; Jingchen Zhai; Beihong Ji ; Viet Hoang Man ...
 
 
A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data 
 
Eitamar Tripto; Yaron Orenstein
 
 
A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains 
 
Janak Sunuwar; Rajeev K Azad
 
 
ProtCHOIR: a tool for proteome-scale generation of homo-oligomers 
 
Pedro H M Torres; Artur D Rossi; Tom L Blundell
 
 
Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts 
 
Miklos Diossy; Zsofia Sztupinszki; Marcin Krzystanek; Judit Borcsok ; Aron C Eklund ...
 
 
An artificial neural network model based on DNA damage response genes to predict outcomes of lower-grade glioma patients 
 
Jian Chen; Xiaojun Qian; Yifu He; Xinghua Han ; Yueyin Pan
 
 
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model 
 
Nikhita Gogate; Daniel Lyman; Amanda Bell; Edmund Cauley ; Keith A Crandall ...
 
 
Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing 
 
Xiyun Jin; Wenyang Zhou; Meng Luo; Pingping Wang ; Zhaochun Xu ...
 
 
A systematic comparison of normalization methods for eQTL analysis 
 
Jiajun Yang; Dongyang Wang; Yanbo Yang; Wenqian Yang ; Weiwei Jin ...
 
 
Benchmarking association analyses of continuous exposures with RNA-seq in observational studies 
 
Tamar Sofer; Nuzulul Kurniansyah; François Aguet; Kristin Ardlie ; Peter Durda ...
 
 
Machine learning builds full-QM precision protein force fields in seconds 
 
Yanqiang Han; Zhilong Wang; Zhiyun Wei; Jinyun Liu ; Jinjin Li
 
 
Methods of privacy-preserving genomic sequencing data alignments 
 
Dandan Lu; Yue Zhang; Ling Zhang; Haiyan Wang ; Wanlin Weng ...
 
 
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants 
 
Ye Wang; Yuchao Jiang; Bing Yao; Kun Huang ; Yunlong Liu ...
 
 
A multi-modal data harmonisation approach for discovery of COVID-19 drug targets 
 
Tyrone Chen; Melcy Philip; Kim-Anh Lê Cao; Sonika Tyagi
 
 
A novel antibacterial peptide recognition algorithm based on BERT 
 
Yue Zhang; Jianyuan Lin; Lianmin Zhao; Xiangxiang Zeng ; Xiangrong Liu
 
 
HelPredictor models single-cell transcriptome to predict human embryo lineage allocation 
 
Pengfei Liang; Lei Zheng; Chunshen Long; Wuritu Yang ; Lei Yang ...
 
 
TSSFinder'fast and accurate ab initio prediction of the core promoter in eukaryotic genomes border= 
 
Mauro de Medeiros Oliveira; Igor Bonadio; Alicia Lie de Melo ; Glaucia Mendes Souza; Alan Mitchell Durham
 
 
A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine border= 
 
Serena Dotolo; Anna Marabotti; Anna Maria Rachiglio ; Riziero Esposito Abate; Marco Benedetto ...
 
 
Corrigendum to: Evaluation of machine learning approaches for cell-type identification from single-cell transcriptomics data 
 
Yixuan Huang; Peng Zhang
 
 
Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms 
 
Yile Huang; Yulong Qiao; Yu Zhao; Yuying Li ; Jie Yuan ...
 
 
Erratum to: Identification of multiple RNAs using feature fusion 
 
Dalwinder Singh; Akansha Madhawan; Joy Roy
 
 
A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing border= 
 
Jialong Liang; Kun Zhang; Jie Yang ; Xianfeng Li; Qinglan Li ...
 
 
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations 
 
Shahid Iqbal; Fuyi Li; Tatsuya Akutsu; David B Ascher ; Geoffrey I Webb ...
 
 
Quercetin for COVID-19 and DENGUE co-infection: a potential therapeutic strategy of targeting critical host signal pathways triggered by SARS-CoV-2 and DENV 
 
Wenjiang Zheng; Hui Wu; Ting Wang; Shaofeng Zhan ; Xiaohong Liu
 
 
SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm 
 
Nabil Ibtehaz; Ishtiaque Ahmed; Md Sabbir Ahmed; M Sohel Rahman ; Rajeev K Azad ...
 
 
Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions 
 
Zulkar Nain; Shital K Barman; Md Moinuddin Sheam; Shifath Bin Syed ; Abdus Samad ...
 
 
A transferable deep learning approach to fast screen potential antiviral drugs against SARS-CoV-2 
 
Shiwei Wang; Qi Sun; Youjun Xu; Jianfeng Pei ; Luhua Lai
 
 
A predictive paradigm for COVID-19 prognosis based on the longitudinal measure of biomarkers 
 
Xin Chen; Wei Gao; Jie Li; Dongfang You ; Zhaolei Yu ...
 
 
Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity 
 
Peilin Jia; Astrid M Manuel; Brisa S Fernandes; Yulin Dai ; Zhongming Zhao
 
 
iAMP-CA2L: a new CNN-BiLSTM-SVM classifier based on cellular automata image for identifying antimicrobial peptides and their functional types 
 
Xuan Xiao; Yu-Tao Shao; Xiang Cheng; Biljana Stamatovic
 
 
PCLasso: a protein complex-based, group lasso-Cox model for accurate prognosis and risk protein complex discovery 
 
Wei Wang; Wei Liu
 
 
Detecting SARS-CoV-2 and its variant strains with a full genome tiling array 
 
Limin Jiang; Yan Guo; Hui Yu; Kendal Hoff ; Xun Ding ...
 
 
Web repositories of natural agents promote pests and pathogenic microbes management 
 
Yin Jin; Zheng Wang; An-Yu Dong; Yuan-Qin Huang ; Ge-Fei Hao ...
 
 
DITHER: an algorithm for Defining IntraTumor Heterogeneity based on EntRopy 
 
Lin Li; Canping Chen; Xiaosheng Wang
 
 
DevOmics: an integrated multi-omics database of human and mouse early embryo 
 
Zhiqiang Yan; Jianting An; Yong Peng; Siming Kong ; Qiang Liu ...
 
 
Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5 border= 
 
Lu Liu; Xikang Feng; Haimei Li ; Shuai Cheng Li; Qiujin Qian ...
 
 
Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects 
 
Lu Huo; Jiao Jiao Li; Ling Chen; Zuguo Yu ; Gyorgy Hutvagner ...
 
 
The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis 
 
Furong Tang; Lichao Zhang; Lei Xu; Quan Zou ; Hailin Feng
 
 
Shall genomic correlation structure be considered in copy number variants detection? 
 
Fei Qin; Xizhi Luo; Guoshuai Cai; Feifei Xiao
 
 
DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19 
 
Xiaoqi Wang; Bin Xin; Weihong Tan; Zhijian Xu ; Kenli Li ...
 
 
A new method to accurately identify single nucleotide variants using small FFPE breast samples border= 
 
Angelo Fortunato; Diego Mallo; Shawn M Rupp ; Lorraine M King; Timothy Hardman ...
 
 
PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture 
 
Xiao Cao; Wenjia He; Zitan Chen; Yifan Li ; Kexin Wang ...
 
 
Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications 
 
Haocheng Ding; Lingsong Meng; Andrew C Liu; Michelle L Gumz ; Andrew J Bryant ...
 
 
Knowledge bases and software support for variant interpretation in precision oncology border= 
 
Florian Borchert; Andreas Mock; Aurelie Tomczak ; Jonas Hügel; Samer Alkarkoukly ...
 
 
Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2 
 
Luyao Qin; Xiao Ding; Yongjie Li; Qingfeng Chen ; Jing Meng ...
 
 
Erratum: usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme 
 
Xi Tang; Tao Zhang; Na Cheng; Huadong Wang ; Chun-Hou Zheng ...
 
 
Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution 
 
Limin Jiang; Hui Yu; Jiawei Li; Jijun Tang ; Yan Guo ...
 
 
REBET: a method to determine the number of cell clusters based on batch effect removal 
 
Zhao-Yu Fang; Cui-Xiang Lin; Yun-Pei Xu; Hong-Dong Li ; Qing-Song Xu
 
 
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets border= 
 
Ali F Alsulami; Pedro H M Torres; Ismail Moghul ; Sheikh Mohammed Arif; Amanda K Chaplin ...
 
 
Understanding structural malleability of the SARS-CoV-2 proteins and relation to the comorbidities 
 
Sagnik Sen; Ashmita Dey; Sanghamitra Bandhyopadhyay; Vladimir N Uversky ; Ujjwal Maulik
 
 
A comprehensive comparative assessment of 3D molecular similarity tools in ligand-based virtual screening 
 
Zhenla Jiang; Jianrong Xu; Aixia Yan; Ling Wang
 
 
An integrated approach for copy number variation discovery in parent'offspring trios 
 
Yongzhuang Liu; Xiaoliang Wu; Yadong Wang
 
 
Human host status inference from temporal microbiome changes via recurrent neural networks 
 
Xingjian Chen; Lingjing Liu; Weitong Zhang; Jianyi Yang ; Ka-Chun Wong
 
 
Consensus clustering of single-cell RNA-seq data by enhancing network affinity border= 
 
Yaxuan Cui; Shaoqiang Zhang; Ying Liang; Xiangyun Wang ; Thomas N Ferraro ...
 
 
LSTM-PHV: prediction of human-virus protein'protein interactions by LSTM with word2vec border= 
 
Sho Tsukiyama; Md Mehedi Hasan; Satoshi Fujii ; Hiroyuki Kurata
 
 
Machine-learning scoring functions trained on complexes dissimilar to the test set already outperform classical counterparts on a blind benchmark border= 
 
Hongjian Li; Gang Lu; Kam-Heung Sze ; Xianwei Su; Wai-Yee Chan ...
 
 
Exosomal ncRNAs profiling of mycobacterial infection identified miRNA-185-5p as a novel biomarker for tuberculosis 
 
Aman Chandra Kaushik; Qiqi Wu; Li Lin; Haibo Li ; Longqi Zhao ...
 
 
Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein 
 
Pengfei Pei; Hongbo Qin; Jialin Chen; Fengli Wang ; Chengzhi He ...
 
 
Evaluation of in silico tools for the prediction of protein and peptide aggregation on diverse datasets 
 
R Prabakaran; Puneet Rawat; Sandeep Kumar; M Michael Gromiha
 
 
MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting border= 
 
Meng Zou; Zhana Duren; Qiuyue Yuan ; Henry Li; Andrew Paul Hutchins ...
 
 
Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins 
 
Hideki Yamaguchi; Yutaka Saito
 
 
EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies 
 
Vishakha Gautam; Aayushi Mittal; Siddhant Kalra; Sanjay Kumar Mohanty ; Krishan Gupta ...
 
 
DeepIPs: comprehensive assessment and computational identification of phosphorylation sites of SARS-CoV-2 infection using a deep learning-based approach 
 
Hao Lv; Fu-Ying Dao; Hasan Zulfiqar; Hao Lin
 
 
Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network 
 
Jing-Yi Li; Shen Jin; Xin-Ming Tu; Yang Ding ; Ge Gao
 
 
A novel graph attention model for predicting frequencies of drug'side effects from multi-view data 
 
Haochen Zhao; Kai Zheng; Yaohang Li; Jianxin Wang
 
 
Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design 
 
Shokouh Rezaei; Yahya Sefidbakht; Vuk Uskoković
 
 
Porpoise: a new approach for accurate prediction of RNA pseudouridine sites 
 
Fuyi Li; Xudong Guo; Peipei Jin; Jinxiang Chen ; Dongxu Xiang ...
 
 
Improving protein fold recognition using triplet network and ensemble deep learning 
 
Yan Liu; Ke Han; Yi-Heng Zhu; Ying Zhang ; Long-Chen Shen ...
 
 
Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation 
 
Chunmei Cui; Yuan Zhou; Qinghua Cui
 
 
Integrative machine learning framework for the identification of cell-specific enhancers from the human genome 
 
Shaherin Basith; Md Mehedi Hasan; Gwang Lee; Leyi Wei ; Balachandran Manavalan
 
 
Erratum to: Analysis, identification and visualization of subgroups in genomics border= 
 
Gunnar Völkel; Simon Laban; Axel Fürstberger; Silke D Kühlwein ; Nensi Ikonomi ...
 
 
A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover border= 
 
Etienne Boileau; Janine Altmüller; Isabel S Naarmann-de Vries ; Christoph Dieterich
 
 
Performance evaluation of transcriptomics data normalization for survival risk prediction border= 
 
Ai Ni; Li-Xuan Qin
 
 
Improved prediction of protein'protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines 
 
Satyajit Mahapatra; Sitanshu Sekhar Sahu
 
 
Published anti-SARS-CoV-2 in vitro hits share common mechanisms of action that synergize with antivirals 
 
Jing Xing; Shreya Paithankar; Ke Liu; Katie Uhl ; Xiaopeng Li ...
 
 
DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads border= 
 
Jiaqi Li; Lei Wei; Xianglin Zhang ; Wei Zhang; Haochen Wang ...
 
 
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases border= 
 
Margaret Staton; Ethalinda Cannon; Lacey-Anne Sanderson ; Jill Wegrzyn; Tavis Anderson ...
 
 
Erratum to: Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins 
 
Hideki Yamaguchi; Yutaka Saito
 
 
ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues 
 
Xuan Liu; Wenbo Chen; Yu Fang; Siqi Yang ; Liuping Chang ...
 
 
QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering 
 
Congting Ye; Danhui Zhao; Wenbin Ye; Xiaohui Wu ; Guoli Ji ...
 
 
Comprehensive analysis of partial methylation domains in colorectal cancer based on single-cell methylation profiles 
 
Yan Huang; Pingping Wang; Wenyang Zhou; Meng Luo ; Zhaochun Xu ...
 
 
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx border= 
 
Seyoon Ko; Ginny X Li; Hyungwon Choi ; Joong-Ho Won
 
 
TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs 
 
Ting Yu; Renmin Han; Zhaoyuan Fang; Zengchao Mu ; Hongyu Zheng ...
 
 
Chromatin loop anchors predict transcript and exon usage border= 
 
Yu Zhang; Yichao Cai; Xavier Roca; Chee Keong Kwoh ; Melissa Jane Fullwood
 
 
AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom 
 
Ritesh Sharma; Sameer Shrivastava; Sanjay Kumar Singh; Abhinav Kumar ; Sonal Saxena ...
 
 
oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data 
 
Danielle Maeser; Robert F Gruener; Rong Stephanie Huang
 
 
High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method 
 
Yongqing Zhang; Zixuan Wang; Yuanqi Zeng; Jiliu Zhou ; Quan Zou
 
 
Corrigendum to: Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein 
 
Pengfei Pei; Hongbo Qin; Jialin Chen; Fengli Wang ; Chengzhi He ...
 
 
Discovering common pathogenetic processes between COVID-19 and diabetes mellitus by differential gene expression pattern analysis border= 
 
Md Rezanur Rahman; Tania Islam; Md Shahjaman ; Md Rafiqul Islam; Salvo Danilo Lombardo ...
 
 
AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches 
 
Yuxuan Pang; Lantian Yao; Jhih-Hua Jhong; Zhuo Wang ; Tzong-Yi Lee
 
 
In silico model for miRNA-mediated regulatory network in cancer 
 
Khandakar Tanvir Ahmed; Jiao Sun; William Chen; Irene Martinez ; Sze Cheng ...
 
 
Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison 
 
Bosheng Song; Fen Li; Yuansheng Liu; Xiangxiang Zeng
 
 
ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides border= 
 
Patrick Brendan Timmons; Chandralal M Hewage
 
 
Deep learning-based real-time detection of novel pathogens during sequencing 
 
Jakub M Bartoszewicz; Ulrich Genske; Bernhard Y Renard
 
 
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network 
 
Hehe Wu; Xiaoyong Pan; Yang Yang; Hong-Bin Shen
 
 
scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species 
 
Xiang Zhou; Hua Chai; Yuansong Zeng; Huiying Zhao ; Yuedong Yang
 
 
bayesynergy: flexible Bayesian modelling of synergistic interaction effects in in vitro drug combination experiments border= 
 
Leiv Rønneberg; Andrea Cremaschi; Robert Hanes ; Jorrit M Enserink; Manuela Zucknick
 
 
Improving distance measures between genomic tracks with mutual proximity 
 
Thomas Haschka; Jean Baptiste Morlot; Leopold Carron; Julien Mozziconacci
 
 
Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption 
 
Shuquan Rao; Ancha Baranova; Hongbao Cao; Jiu Chen ; Xiangrong Zhang ...
 
 
Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network 
 
Trinh-Trung-Duong Nguyen; Duc-Khanh Nguyen; Yu-Yen Ou
 
 
GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes 
 
Ruiqi Lyu; Jianle Sun; Dong Xu; Qianxue Jiang ; Chaochun Wei ...
 
 
Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology 
 
Amarinder Singh Thind; Isha Monga; Prasoon Kumar Thakur; Pallawi Kumari ; Kiran Dindhoria ...
 
 
Circular RNAs and complex diseases: from experimental results to computational models border= 
 
Chun-Chun Wang; Chen-Di Han; Qi Zhao ; Xing Chen
 
 
 
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