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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 24 Issue 1
 
January 2023
 
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Articles
 
 
 
 
RLBind: a deep learning method to predict RNA'ligand binding sites 
 
Kaili Wang ; Renyi Zhou; Yifan Wu; Min Li
 
 
 
Label-free proteome quantification and evaluation 
 
Jianbo Fu ; Qingxia Yang; Yongchao Luo; Song Zhang; Jing Tang ...
 
 
 
HN-PPISP: a hybrid network based on MLP-Mixer for protein'protein interaction site prediction 
 
Yan Kang; Yulong Xu; Xinchao Wang; Bin Pu ; Xuekun Yang ...
 
 
 
IPPF-FE: an integrated peptide and protein function prediction framework based on fused features and ensemble models 
 
Han Yu; Xiaozhou Luo
 
 
 
Benchmarking cell-type clustering methods for spatially resolved transcriptomics data border= 
 
Andrew Cheng; Guanyu Hu; Wei Vivian Li
 
 
 
 
Multiple errors correction for position-limited DNA sequences with GC balance and no homopolymer for DNA-based data storage 
 
Xiayang Li; Moxuan Chen; Huaming Wu
 
 
 
PlDBPred: a novel computational model for discovery of DNA binding proteins in plants 
 
Upendra Kumar Pradhan; Prabina Kumar Meher; Sanchita Naha; Soumen Pal ; Ajit Gupta ...
 
 
 
>From single- to multi-omics: future research trends in medicinal plants border= 
 
Lifang Yang ; Ye Yang; Luqi Huang; Xiuming Cui; Yuan Liu
 
 
 
PhaTYP: predicting the lifestyle for bacteriophages using BERT border= 
 
Jiayu Shang; Xubo Tang; Yanni Sun
 
 
 
SNRMPACDC: computational model focused on Siamese network and random matrix projection for anticancer synergistic drug combination prediction 
 
Tian-Hao Li; Chun-Chun Wang; Li Zhang; Xing Chen
 
 
 
 
Cancer subtyping with heterogeneous multi-omics data via hierarchical multi-kernel learning 
 
Yifang Wei; Lingmei Li; Xin Zhao ; Haitao Yang; Jian Sa ...
 
 
 
Adaptive risk-aware sharable and individual subspace learning for cancer survival analysis with multi-modality data 
 
Zhangxin Zhao; Qianjin Feng ; Yu Zhang; Zhenyuan Ning
 
 
 
Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience border= 
 
Marwan Abdellah ; Juan José García Cantero; Nadir Román Guerrero; Alessandro Foni; Jay S Coggan ...
 
 
 
Extraction of microRNA'target interaction sentences from biomedical literature by deep learning approach 
 
Mengqi Luo; Shangfu Li; Yuxuan Pang; Lantian Yao ; Renfei Ma ...
 
 
 
DeepHomo2.0: improved protein'protein contact prediction of homodimers by transformer-enhanced deep learning 
 
Peicong Lin; Yumeng Yan; Sheng-You Huang
 
 
 
Validation of transcriptome signature reversion for drug repurposing in oncology border= 
 
Karel K M Koudijs; Stefan Böhringer; Henk-Jan Guchelaar
 
 
 
SPRDA: a link prediction approach based on the structural perturbation to infer disease-associated Piwi-interacting RNAs 
 
Kai Zheng; Xin-Lu Zhang; Lei Wang; Zhu-Hong You ; Bo-Ya Ji ...
 
 
 
Multi-view spectral clustering with latent representation learning for applications on multi-omics cancer subtyping 
 
Shuguang Ge; Jian Liu; Yuhu Cheng ; Xiaojing Meng; Xuesong Wang
 
 
 
Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework 
 
Wenchuang He; Kunli Xiang ; Caijin Chen; Jie Wang; Zhiqiang Wu
 
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Deep generative modeling and clustering of single cell Hi-C data 
 
Qiao Liu ; Wanwen Zeng; Wei Zhang; Sicheng Wang; Hongyang Chen ...
 
 
 
CLIP: accurate prediction of disordered linear interacting peptides from protein sequences using co-evolutionary information 
 
Zhenling Peng; Zixia Li; Qiaozhen Meng; Bi Zhao ; Lukasz Kurgan
 
 
 
Dimensionality reduction approach for many-objective epistasis analysis 
 
Cheng-Hong Yang; Ming-Feng Hou; Li-Yeh Chuang ; Cheng-San Yang; Yu-Da Lin
 
 
 
GADRP: graph convolutional networks and autoencoders for cancer drug response prediction 
 
Hong Wang; Chong Dai ; Yuqi Wen; Xiaoqi Wang; Wenjuan Liu ...
 
 
 
RAMP: response-aware multi-task learning with contrastive regularization for cancer drug response prediction 
 
Kanggeun Lee; Dongbin Cho; Jinho Jang; Kang Choi ; Hyoung-oh Jeong ...
 
 
 
Improved model quality assessment using sequence and structural information by enhanced deep neural networks 
 
Jun Liu; Kailong Zhao; Guijun Zhang
 
 
 
Succinylated lysine residue prediction revisited 
 
Shehab Sarar Ahmed ; Zaara Tasnim Rifat; M Saifur Rahman; M Sohel Rahman
 
 
 
A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer's disease network 
 
Softya Sebastian; Swarup Roy; Jugal Kalita
 
 
 
Virus classification for viral genomic fragments using PhaGCN2 
 
Jing-Zhe Jiang ; Wen-Guang Yuan; Jiayu Shang; Ying-Hui Shi; Li-Ling Yang ...
 
 
 
Concept drift detection in toxicology datasets using discriminative subgraph-based drift detector 
 
Vandana Bharti; Shabari S Nair; Akshat Jain; Kaushal Kumar Shukla ; Bhaskar Biswas
 
 
 
Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis 
 
Danni Hong; Hongli Lin; Lifang Liu ; Muya Shu; Jianwu Dai ...
 
 
 
RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization border= 
 
Guo-Hua Yuan ; Ying Wang; Guang-Zhong Wang; Li Yang
 
 
 
SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning 
 
Xin Zhang; Lesong Wei; Xiucai Ye; Kai Zhang ; Saisai Teng ...
 
 
 
Pdif-mediated antibiotic resistance genes transfer in bacteria identified by pdifFinder 
 
Mengjie Shao; Nanjiao Ying; Qian Liang ; Nan Ma; Sebastian Leptihn ...
 
 
 
A comprehensive assessment of cell type-specific differential expression methods in bulk data border= 
 
Guanqun Meng ; Wen Tang; Emina Huang; Ziyi Li; Hao Feng
 
 
 
Grain protein function prediction based on self-attention mechanism and bidirectional LSTM 
 
Jing Liu; Xinghua Tang; Xiao Guan
 
 
 
Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes border= 
 
Simon Orozco-Arias ; Luis Humberto Lopez-Murillo; Mariana S Candamil-Cortés; Maradey Arias; Paula A Jaimes ...
 
 
 
VirusRecom: an information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2 
 
Zhi-Jian Zhou; Chen-Hui Yang; Sheng-Bao Ye; Xiao-Wei Yu ; Ye Qiu ...
 
 
 
A review of methods for predicting DNA N6-methyladenine sites 
 
Ke Han; Jianchun Wang; Yu Wang ; Lei Zhang; Mengyao Yu ...
 
 
 
Multimodal data fusion based on IGERNNC algorithm for detecting pathogenic brain regions and genes in Alzheimer's disease 
 
Shuaiqun Wang; Kai Zheng ; Wei Kong; Ruiwen Huang; Lulu Liu ...
 
 
 
A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function 
 
Zechen Wang; Liangzhen Zheng; Sheng Wang; Mingzhi Lin ; Zhihao Wang ...
 
 
 
MARPPI: boosting prediction of protein'protein interactions with multi-scale architecture residual network 
 
Xue Li; Peifu Han; Wenqi Chen ; Changnan Gao; Shuang Wang ...
 
 
 
DPADM: a novel algorithm for detecting drug-pathway associations based on high-throughput transcriptional response to compounds 
 
Yishu Wang; Juan Qi ; Dongmei Ai
 
 
 
CRMSS: predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features 
 
Lishen Zhang; Chengqian Lu; Min Zeng ; Yaohang Li; Jianxin Wang
 
 
 
CapsNet-LDA: predicting lncRNA-disease associations using attention mechanism and capsule network based on multi-view data 
 
Zequn Zhang; Junlin Xu ; Yanan Wu; Niannian Liu; Yinglong Wang ...
 
 
 
Vir2Drug: a drug repurposing framework based on protein similarities between pathogens border= 
 
George Minadakis; Marios Tomazou; Nikolas Dietis; George M Spyrou
 
 
 
Incomplete time-series gene expression in integrative study for islet autoimmunity prediction 
 
Khandakar Tanvir Ahmed; Sze Cheng; Qian Li; Jeongsik Yong ; Wei Zhang
 
 
 
RefTM: reference-guided topic modeling of single-cell chromatin accessibility data 
 
Zheng Zhang; Shengquan Chen; Zhixiang Lin
 
 
 
Predicting potential interactions between lncRNAs and proteins via combined graph auto-encoder methods 
 
Jingxuan Zhao; Jianqiang Sun; Stella C Shuai; Qi Zhao ; Jianwei Shuai
 
 
 
From multi-omics data to the cancer druggable gene discovery: a novel machine learning-based approach 
 
Hai Yang; Lipeng Gan; Rui Chen ; Dongdong Li; Jing Zhang ...
 
 
 
A deep transfer learning-based protocol accelerates full quantum mechanics calculation of protein 
 
Yanqiang Han; Zhilong Wang ; An Chen; Imran Ali; Junfei Cai ...
 
 
 
Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile 
 
Sumeet Patiyal; Anjali Dhall; Khushboo Bajaj; Harshita Sahu; Gajendra P S Raghava
 
 
 
DMPPred: a tool for identification of antigenic regions responsible for inducing type 1 diabetes mellitus 
 
Nishant Kumar; Sumeet Patiyal; Shubham Choudhury; Ritu Tomer ; Anjali Dhall ...
 
 
 
Predicting miRNA-disease associations based on lncRNA'miRNA interactions and graph convolution networks 
 
Wengang Wang; Hailin Chen
 
 
 
AdaPPI: identification of novel protein functional modules via adaptive graph convolution networks in a protein'protein interaction network 
 
Hongwei Chen; Yunpeng Cai; Chaojie Ji; Gurudeeban Selvaraj ; Dongqing Wei ...
 
 
 
Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism 
 
Yanan Tian; Xiaorui Wang; Xiaojun Yao ; Huanxiang Liu; Ying Yang
 
 
 
Recent advances in cancer fusion transcript detection border= 
 
Ryley Dorney; Bijay P Dhungel; John E J Rasko; Lionel Hebbard; Ulf Schmitz
 
 
 
DrugAI: a multi-view deep learning model for predicting drug'target activating/inhibiting mechanisms 
 
Siqin Zhang; Kuo Yang; Zhenhong Liu; Xinxing Lai ; Zhen Yang ...
 
 
 
dSCOPE: a software to detect sequences critical for liquid'liquid phase separation 
 
Kai Yu; Zekun Liu; Haoyang Cheng ; Shihua Li; Qingfeng Zhang ...
 
 
 
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants 
 
Fang Ge; Chen Li ; Shahid Iqbal; Arif Muhammad; Fuyi Li ...
 
 
 
A comprehensive review on knowledge graphs for complex diseases 
 
Yang Yang ; Yuwei Lu; Wenying Yan
 
 
 
DNA-MP: a generalized DNA modifications predictor for multiple species based on powerful sequence encoding method 
 
Muhammad Nabeel Asim; Muhammad Ali Ibrahim ; Ahtisham Fazeel; Andreas Dengel; Sheraz Ahmed
 
 
 
Multi-view contrastive heterogeneous graph attention network for lncRNA'disease association prediction 
 
Xiaosa Zhao; Jun Wu; Xiaowei Zhao; Minghao Yin
 
 
 
Improving the performance of single-cell RNA-seq data mining based on relative expression orderings border= 
 
Yuanyuan Chen; Hao Zhang; Xiao Sun
 
 
 
Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers border= 
 
Wenjie Du; Xiaoting Yang; Di Wu; FenFen Ma ; Baicheng Zhang ...
 
 
 
Identification of vital chemical information via visualization of graph neural networks 
 
Yimeng Wang; Mengting Huang; Hua Deng ; Weihua Li; Zengrui Wu ...
 
 
 
Correction to: siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers 
 
 
 
 
SAM-DTA: a sequence-agnostic model for drug'target binding affinity prediction 
 
Zhiqiang Hu; Wenfeng Liu ; Chenbin Zhang; Jiawen Huang; Shaoting Zhang ...
 
 
 
LncRNA-disease association identification using graph auto-encoder and learning to rank 
 
Qi Liang; Wenxiang Zhang; Hao Wu; Bin Liu
 
 
 
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly border= 
 
Denis Beslic; Georg Tscheuschner; Bernhard Y Renard; Michael G Weller ; Thilo Muth
 
 
 
A fast and powerful linear mixed model approach for genotype-environment interaction tests in large-scale GWAS 
 
Wujuan Zhong; Aparna Chhibber; Lan Luo ; Devan V Mehrotra; Judong Shen
 
 
 
ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications border= 
 
Giulia Pais ; Giulio Spinozzi; Daniela Cesana; Fabrizio Benedicenti; Alessandra Albertini ...
 
 
 
spaCI: deciphering spatial cellular communications through adaptive graph model border= 
 
Ziyang Tang; Tonglin Zhang; Baijian Yang ; Jing Su; Qianqian Song
 
 
 
GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation 
 
Min Li; Baoying Zhao ; Rui Yin; Chengqian Lu; Fei Guo ...
 
 
 
CODA: a combo-Seq data analysis workflow border= 
 
Marta Nazzari; Duncan Hauser; Marcel van Herwijnen; Mírian Romitti ; Daniel J Carvalho ...
 
 
 
Learning single-cell chromatin accessibility profiles using meta-analytic marker genes border= 
 
Risa Karakida Kawaguchi ; Ziqi Tang; Stephan Fischer; Chandana Rajesh; Rohit Tripathy ...
 
 
 
GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels 
 
Chun-Jie Liu; Fei-Fei Hu; Gui-Yan Xie; Ya-Ru Miao ; Xin-Wen Li ...
 
 
 
DRONet: effectiveness-driven drug repositioning framework using network embedding and ranking learning 
 
Kuo Yang; Yuxia Yang; Shuyue Fan ; Jianan Xia; Qiguang Zheng ...
 
 
 
Incorporating higher order network structures to improve miRNA'disease association prediction based on functional modularity 
 
Yizhou He; Yue Yang ; Xiaorui Su; Bowei Zhao; Shengwu Xiong ...
 
 
 
Improving therapeutic synergy score predictions with adverse effects using multi-task heterogeneous network learning border= 
 
Yang Yue; Yongxuan Liu; Luoying Hao; Huangshu Lei ; Shan He
 
 
 
Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments 
 
Ruyun Hu; Lihao Fu; Yongcan Chen ; Junyu Chen; Yu Qiao ...
 
 
 
CCSynergy: an integrative deep-learning framework enabling context-aware prediction of anti-cancer drug synergy 
 
Sayed-Rzgar Hosseini; Xiaobo Zhou
 
 
 
Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire 
 
Yu Zhao; Bing He; Zhimeng Xu; Yidan Zhang ; Xuan Zhao ...
 
 
 
Matrix reconstruction with reliable neighbors for predicting potential MiRNA'disease associations 
 
Hailin Feng; Dongdong Jin; Jian Li ; Yane Li; Quan Zou ...
 
 
 
Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data 
 
Siqi Chen; Xuhua Yan ; Ruiqing Zheng; Min Li
 
 
 
Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network 
 
Chengqian Lu; Lishen Zhang ; Min Zeng; Wei Lan; Guihua Duan ...
 
 
 
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC'MS global metabolomics data 
 
Yao Lu; Zhiqiang Pang; Jianguo Xia
 
 
 
Personalized immune subtypes based on machine learning predict response to checkpoint blockade in gastric cancer 
 
Weibin Huang; Yuhui Zhang; Songyao Chen; Haofan Yin ; Guangyao Liu ...
 
 
 
BloodNet: An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference 
 
Huiyu Li; Chen Shen; Gongji Wang ; Qinru Sun; Kai Yu ...
 
 
 
HCovDock: an efficient docking method for modeling covalent protein'ligand interactions 
 
Qilong Wu; Sheng-You Huang
 
 
 
Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames border= 
 
Yiming Xu; Bowen Zheng; Xiaohong Liu; Tao Wu ; Jinxiu Ju ...
 
 
 
R2-DDI: relation-aware feature refinement for drug'drug interaction prediction 
 
Jiacheng Lin; Lijun Wu; Jinhua Zhu ; Xiaobo Liang; Yingce Xia ...
 
 
 
LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism 
 
Tianyuan Liu; Bohao Zou ; Manman He; Yongfei Hu; Yiying Dou ...
 
 
 
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning border= 
 
Bailing Zhou; Maolin Ding; Jing Feng; Baohua Ji ; Pingping Huang ...
 
 
 
SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level 
 
Lei Sun; Gongming Wang; Zhihua Zhang
 
 
 
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors 
 
Dong Wang; Zhenxing Wu; Chao Shen; Lingjie Bao ; Hao Luo ...
 
 
 
An evolution-based machine learning to identify cancer type-specific driver mutations 
 
Donghyo Kim; Doyeon Ha; Kwanghwan Lee ; Heetak Lee; Inhae Kim ...
 
 
 
To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities 
 
Jiayin Zhou; Wen Song ; Qichao Tu
 
 
 
Logistic tensor decomposition with sparse subspace learning for prediction of multiple disease types of human'virus protein'protein interactions 
 
Yingjun Ma; Junjiang Zhong
 
 
 
A Bayesian model for identifying cancer subtypes from paired methylation profiles border= 
 
Yetian Fan; April S Chan; Jun Zhu; Suet Yi Leung ; Xiaodan Fan
 
 
 
Advances in the field of phage-based therapy with special emphasis on computational resources 
 
Nisha Bajiya; Anjali Dhall; Suchet Aggarwal ; Gajendra P S Raghava
 
 
 
SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants 
 
Xiao Fan; Hongbing Pan; Alan Tian ; Wendy K Chung; Yufeng Shen
 
 
 
Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs 
 
Zhenshuang Tang; Lilin Yin ; Dong Yin; Haohao Zhang; Yuhua Fu ...
 
 
 
A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications 
 
Bihan Shen; Fangyoumin Feng; Kunshi Li; Ping Lin ; Liangxiao Ma ...
 
 
 
Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning 
 
Xi-Liang Zhu; Lin-Xia Bao; Min-Qi Xue ; Ying-Ying Xu
 
 
 
Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis 
 
Lingling Wang; Lei Xu; Zhe Wang ; Tingjun Hou; Haiping Hao ...
 
 
 
bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data border= 
 
Ilias Moutsopoulos ; Eleanor C Williams; Irina I Mohorianu
 
 
 
A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants 
 
Chonghao Wang; Jing Zhang ; Werner Pieter Veldsman; Xin Zhou; Lu Zhang
 
 
 
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets border= 
 
Erik Christensen; Ping Luo; Andrei Turinsky; Mia Husić ; Alaina Mahalanabis ...
 
 
 
Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning 
 
Zerun Lin; Le Ou-Yang
 
 
 
Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion border= 
 
Anna Dal Molin; Caterina Tretti Parenzan; Enrico Gaffo; Cristina Borin ; Elena Boldrin ...
 
 
 
A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets 
 
Sanghun Lee; Georg Hahn; Julian Hecker ; Sharon M Lutz; Kristina Mullin ...
 
 
 
CasANGCL: pre-training and fine-tuning model based on cascaded attention network and graph contrastive learning for molecular property prediction 
 
Zixi Zheng; Yanyan Tan ; Hong Wang; Shengpeng Yu; Tianyu Liu ...
 
 
 
Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data border= 
 
Tim D Rose; Nikolai Köhler; Lisa Falk ; Lucie Klischat; Olga E Lazareva ...
 
 
 
Metapath-aggregated heterogeneous graph neural network for drug'target interaction prediction 
 
Mei Li; Xiangrui Cai ; Sihan Xu; Hua Ji
 
 
 
scGMAAE: Gaussian mixture adversarial autoencoders for diversification analysis of scRNA-seq data 
 
Hai-Yun Wang; Jian-Ping Zhao ; Chun-Hou Zheng; Yan-Sen Su
 
 
 
Predicting lncRNA'disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation 
 
Guo-Bo Xie; Rui-Bin Chen ; Zhi-Yi Lin; Guo-Sheng Gu; Jun-Rui Yu ...
 
 
 
DSN-DDI: an accurate and generalized framework for drug'drug interaction prediction by dual-view representation learning 
 
Zimeng Li; Shichao Zhu; Bin Shao; Xiangxiang Zeng ; Tong Wang ...
 
 
 
Systematic benchmarking of statistical methods to assess differential expression of circular RNAs border= 
 
Alessia Buratin ; Stefania Bortoluzzi; Enrico Gaffo
 
 
 
Benchmarking of computational methods for predicting circRNA-disease associations 
 
Wei Lan; Yi Dong ; Hongyu Zhang; Chunling Li; Qingfeng Chen ...
 
 
 
slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences border= 
 
Bo Song; Hao Li; Mengyun Jiang; Zhongtian Gao ; Suikang Wang ...
 
 
 
From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies? 
 
Joel Defo; Denis Awany; Raj Ramesar
 
 
 
Deleterious synonymous mutation identification based on selective ensemble strategy 
 
Lihua Wang; Tao Zhang; Lihong Yu; Chun-Hou Zheng ; Wenguang Yin ...
 
 
 
Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA border= 
 
Eva María Trinidad ; Enrique Vidal; Esther Coronado; Anna Esteve-Codina; Victoria Castel ...
  ;
 
 
Critical review of conformational B-cell epitope prediction methods 
 
Gabriel Cia; Fabrizio Pucci; Marianne Rooman
 
 
 
Benchmarking differential abundance analysis methods for correlated microbiome sequencing data 
 
Lu Yang; Jun Chen
 
 
 
Comparative epigenome analysis using Infinium DNA methylation BeadChips 
 
Wubin Ding; Diljeet Kaur ; Steve Horvath; Wanding Zhou
 
 
 
Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism 
 
Bo Yang; Hailin Chen
 
 
 
The hitchhikers' guide to RNA sequencing and functional analysis 
 
Jiung-Wen Chen; Lisa Shrestha; George Green; André Leier ; Tatiana T Marquez-Lago
 
 
 
Correction to: VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants 
 
 
 
 
Leveraging scaffold information to predict protein'ligand binding affinity with an empirical graph neural network 
 
Chunqiu Xia; Shi-Hao Feng; Ying Xia ; Xiaoyong Pan; Hong-Bin Shen
 
 
 
Structure-preserved dimension reduction using joint triplets sampling for multi-batch integration of single-cell transcriptomic data 
 
Xinyi Xu; Xiangjie Li
 
 
 
Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings border= 
 
Wayland Yeung; Zhongliang Zhou; Sheng Li ; Natarajan Kannan
 
 
 
AFP-MFL: accurate identification of antifungal peptides using multi-view feature learning 
 
Yitian Fang; Fan Xu; Lesong Wei ; Yi Jiang; Jie Chen ...
 
 
 
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy 
 
Wenxuan Deng; Bolun Li ; Jiawei Wang; Wei Jiang; Xiting Yan ...
 
 
 
A novel strategy for designing the magic shotguns for distantly related target pairs 
 
Yongchao Luo; Panpan Wang; Minjie Mou; Hanqi Zheng; Jiajun Hong ...
 < /td>
 
 
scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network 
 
Jing Wang; Junfeng Xia; Haiyun Wang; Yansen Su ; Chun-Hou Zheng
 
 
 
Tracing human life trajectory using gut microbial communities by context-aware deep learning 
 
Haohong Zhang; Hui Chong; Qingyang Yu ; Yuguo Zha; Mingyue Cheng ...
 
 
 
RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning border= 
 
Shujun He ; Baizhen Gao; Rushant Sabnis; Qing Sun
 
 
 
Modeling and analyzing single-cell multimodal data with deep parametric inference 
 
Huan Hu; Zhen Feng; Hai Lin; Junjie Zhao; Yaru Zhang ...
 
 
 
Prediction of anticancer peptides based on an ensemble model of deep learning and machine learning using ordinal positional encoding 
 
Qitong Yuan; Keyi Chen; Yimin Yu; Nguyen Quoc Khanh Le ; Matthew Chin Heng Chua
 
 
 
Integrated mRNA sequence optimization using deep learning 
 
Haoran Gong; Jianguo Wen; Ruihan Luo ; Yuzhou Feng; JingJing Guo ...
 
 
 
A social theory-enhanced graph representation learning framework for multitask prediction of drug'drug interactions 
 
Yue-Hua Feng; Shao-Wu Zhang ; Yi-Yang Feng; Qing-Qing Zhang; Ming-Hui Shi ...
 
 
 
Computational model for disease research 
 
Xing Chen ; Li Huang
 
 
 
Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies border= 
 
Wayland Yeung ; Zhongliang Zhou; Liju Mathew; Nathan Gravel; Rahil Taujale ...
 
 
 
GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability 
 
Kai Wang
 
 
 
Reducing false positive rate of docking-based virtual screening by active learning 
 
Lei Wang; Shao-Hua Shi; Hui Li ; Xiang-Xiang Zeng; Su-You Liu ...
 
 
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