Works matching IS 14675463 AND DT 2022 AND VI 23 AND IP 5

Results: 137

Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac400

By:

Mercatelli, Daniele;
Cabrelle, Chiara;
Veltri, Pierangelo;
Giorgi, Federico M;
Guzzi, Pietro H

Publication type:

Article

TPD: a web tool for tipping-point detection based on dynamic network biomarker.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac399

By:

Chen, Pei;
Zhong, Jiayuan;
Yang, Kun;
Zhang, Xuhang;
Chen, Yingqi;
Liu, Rui

Publication type:

Article

SCDD: a novel single-cell RNA-seq imputation method with diffusion and denoising.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac398

By:

Liu, Jian;
Pan, Yichen;
Ruan, Zhihan;
Guo, Jun

Publication type:

Article

iLoc-miRNA: extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac395

By:

Zhang, Zhao-Yue;
Ning, Lin;
Ye, Xiucai;
Yang, Yu-He;
Futamura, Yasunori;
Sakurai, Tetsuya;
Lin, Hao

Publication type:

Article

novel circRNA-miRNA association prediction model based on structural deep neural network embedding.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac391

By:

Guo, Lu-Xiang;
You, Zhu-Hong;
Wang, Lei;
Yu, Chang-Qing;
Zhao, Bo-Wei;
Ren, Zhong-Hao;
Pan, Jie

Publication type:

Article

Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac389

By:

Shu, Hantao;
Ding, Fan;
Zhou, Jingtian;
Xue, Yexiang;
Zhao, Dan;
Zeng, Jianyang;
Ma, Jianzhu

Publication type:

Article

machine learning framework based on multi-source feature fusion for circRNA-disease association prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac388

By:

Wang, Lei;
Wong, Leon;
Li, Zhengwei;
Huang, Yuan;
Su, Xiaorui;
Zhao, Bowei;
You, Zhuhong

Publication type:

Article

OncoPubMiner: a platform for mining oncology publications.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac383

By:

Xu, Quan;
Liu, Yueyue;
Hu, Jifang;
Duan, Xiaohong;
Song, Niuben;
Zhou, Jiale;
Zhai, Jincheng;
Su, Junyan;
Liu, Siyao;
Chen, Fan;
Zheng, Wei;
Guo, Zhongjia;
Li, Hexiang;
Zhou, Qiming;
Niu, Beifang

Publication type:

Article

Not all T cell epitopes are equally desired: a review of in silico tools for the prediction of cytokine-inducing potential of T-cell epitopes.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac382

By:

Dhanda, Sandeep Kumar;
Malviya, Jitendra;
Gupta, Sudheer

Publication type:

Article

TSomVar: a tumor-only somatic and germline variant identification method with random forest.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac381

By:

Shi, Shuo;
Wang, Qi;
Shang, Yunfei;
Bu, Congfan;
Lu, Mingming;
Jiang, Meiye;
Zhang, Hao;
Yu, Shuhuan;
Zeng, Jingyao;
Zhang, Zaichao;
Du, Zhenglin;
Xiao, Jingfa

Publication type:

Article

GraphCDA: a hybrid graph representation learning framework based on GCN and GAT for predicting disease-associated circRNAs.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac379

By:

Dai, Qiguo;
Liu, Ziqiang;
Wang, Zhaowei;
Duan, Xiaodong;
Guo, Maozu

Publication type:

Article

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac377

By:

Han, Wenkai;
Cheng, Yuqi;
Chen, Jiayang;
Zhong, Huawen;
Hu, Zhihang;
Chen, Siyuan;
Zong, Licheng;
Hong, Liang;
Chan, Ting-Fung;
King, Irwin;
Gao, Xin;
Li, Yu

Publication type:

Article

PEcnv: accurate and efficient detection of copy number variations of various lengths.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac375

By:

Wang, Xuwen;
Xu, Ying;
Liu, Ruoyu;
Lai, Xin;
Liu, Yuqian;
Wang, Shenjie;
Zhang, Xuanping;
Wang, Jiayin

Publication type:

Article

Letter to the editor: evaluating computational tools for lncRNA identification on independent datasets.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac371

By:

Zheng, Hansi;
Li, Xiaoman;
Hu, Haiyan

Publication type:

Article

Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac368

By:

Agapito, Giuseppe;
Pastrello, Chiara;
Niu, Yun;
Jurisica, Igor

Publication type:

Article

Identifying and characterizing drug sensitivity-related lncRNA-TF-gene regulatory triplets.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac366

By:

Hu, Congxue;
Xu, Yingqi;
Li, Feng;
Mi, Wanqi;
Yu, He;
Wang, Xinran;
Wen, Xin;
Chen, Shuaijun;
Li, Xia;
Xu, Yanjun;
Zhang, Yunpeng

Publication type:

Article

chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac365

By:

Liu, Fei;
Jiang, Xiangkang;
Yang, Jingyuan;
Tao, Jiawei;
Zhang, Mao

Publication type:

Article

biomedical knowledge graph-based method for drug–drug interactions prediction through combining local and global features with deep neural networks.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac363

By:

Ren, Zhong-Hao;
You, Zhu-Hong;
Yu, Chang-Qing;
Li, Li-Ping;
Guan, Yong-Jian;
Guo, Lu-Xiang;
Pan, Jie

Publication type:

Article

Learning global dependencies and multi-semantics within heterogeneous graph for predicting disease-related lncRNAs.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac361

By:

Xuan, Ping;
Wang, Shuai;
Cui, Hui;
Zhao, Yue;
Zhang, Tiangang;
Wu, Peiliang

Publication type:

Article

novel pathway mutation perturbation score predicts the clinical outcomes of immunotherapy.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac360

By:

Li, Xiangmei;
He, Yalan;
Wu, Jiashuo;
Qiu, Jiayue;
Li, Ji;
Wang, Qian;
Jiang, Ying;
Han, Junwei

Publication type:

Article

Large-scale comparison of machine learning algorithms for target prediction of natural products.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac359

By:

Liang, Lu;
Liu, Ye;
Kang, Bo;
Wang, Ru;
Sun, Meng-Yu;
Wu, Qi;
Meng, Xiang-Fei;
Lin, Jian-Ping

Publication type:

Article

Updated review of advances in microRNAs and complex diseases: taxonomy, trends and challenges of computational models.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac358

By:

Huang, Li;
Zhang, Li;
Chen, Xing

Publication type:

Article

merged molecular representation deep learning method for blood–brain barrier permeability prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac357

By:

Tang, Qiang;
Nie, Fulei;
Zhao, Qi;
Chen, Wei

Publication type:

Article

comparative analysis of amino acid encoding schemes for the prediction of flexible length linear B-cell epitopes.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac356

By:

Sahu, Tanmaya Kumar;
Meher, Prabina Kumar;
Choudhury, Nalini Kanta;
Rao, Atmakuri Ramakrishna

Publication type:

Article

Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac355

By:

Gable, Annika L;
Szklarczyk, Damian;
Lyon, David;
Rodrigues, João F Matias;
Mering, Christian von

Publication type:

Article

Deciphering signatures of natural selection via deep learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac354

By:

Qin, Xinghu;
Chiang, Charleston W K;
Gaggiotti, Oscar E

Publication type:

Article

Multiple similarity drug–target interaction prediction with random walks and matrix factorization.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac353

By:

Liu, Bin;
Papadopoulos, Dimitrios;
Malliaros, Fragkiskos D;
Tsoumakas, Grigorios;
Papadopoulos, Apostolos N

Publication type:

Article

SADeepcry: a deep learning framework for protein crystallization propensity prediction using self-attention and auto-encoder networks.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac352

By:

Wang, Shaokai;
Zhao, Haochen

Publication type:

Article

Profiling prediction of nuclear receptor modulators with multi-task deep learning methods: toward the virtual screening.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac351

By:

Wang, Jiye;
Lou, Chaofeng;
Liu, Guixia;
Li, Weihua;
Wu, Zengrui;
Tang, Yun

Publication type:

Article

ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac350

By:

Yan, Huihui;
Xie, Yuanyuan;
Liu, Yao;
Yuan, Leer;
Sheng, Rong

Publication type:

Article

IgIDivA: immunoglobulin intraclonal diversification analysis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac349

By:

Zaragoza-Infante, Laura;
Junet, Valentin;
Pechlivanis, Nikos;
Fragkouli, Styliani-Christina;
Amprachamian, Serovpe;
Koletsa, Triantafyllia;
Chatzidimitriou, Anastasia;
Papaioannou, Maria;
Stamatopoulos, Kostas;
Agathangelidis, Andreas;
Psomopoulos, Fotis

Publication type:

Article

G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac348

By:

Sahu, Tanmaya Kumar;
Singh, Amit Kumar;
Mittal, Shikha;
Jha, Shailendra Kumar;
Kumar, Sundeep;
Jacob, Sherry Rachel;
Singh, Kuldeep

Publication type:

Article

DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac347

By:

Zou, Guanhua;
Lin, Yilong;
Han, Tianyang;
Ou-Yang, Le

Publication type:

Article

Identifying the kind behind SMILES—anatomical therapeutic chemical classification using structure-only representations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac346

By:

Cao, Yi;
Yang, Zhen-Qun;
Zhang, Xu-Lu;
Fan, Wenqi;
Wang, Yaowei;
Shen, Jiajun;
Wei, Dong-Qing;
Li, Qing;
Wei, Xiao-Yong

Publication type:

Article

Metric learning for comparing genomic data with triplet network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac345

By:

Ma, Zhi;
Lu, Yang Young;
Wang, Yiwen;
Lin, Renhao;
Yang, Zizi;
Zhang, Fang;
Wang, Ying

Publication type:

Article

genetic algorithm-aided three-stage ensemble learning method identified a robust survival risk score in patients with glioma.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac344

By:

Zhu, Sujie;
Kong, Weikaixin;
Zhu, Jie;
Huang, Liting;
Wang, Shixin;
Bi, Suzhen;
Xie, Zhengwei

Publication type:

Article

Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac343

By:

Sidorczuk, Katarzyna;
Gagat, Przemysław;
Pietluch, Filip;
Kała, Jakub;
Rafacz, Dominik;
Bąkała, Laura;
Słowik, Jadwiga;
Kolenda, Rafał;
Rödiger, Stefan;
Fingerhut, Legana C H W;
Cooke, Ira R;
Mackiewicz, Paweł;
Burdukiewicz, Michał

Publication type:

Article

R5hmCFDV: computational identification of RNA 5-hydroxymethylcytosine based on deep feature fusion and deep voting.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac341

By:

Shi, Hongyan;
Zhang, Shengli;
Li, Xinjie

Publication type:

Article

SFGAE: a self-feature-based graph autoencoder model for miRNA–disease associations prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac340

By:

Ma, Mingyuan;
Na, Sen;
Zhang, Xiaolu;
Chen, Congzhou;
Xu, Jin

Publication type:

Article

Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac332

By:

Toro-Domínguez, Daniel;
Martorell-Marugán, Jordi;
Martinez-Bueno, Manuel;
López-Domínguez, Raúl;
Carnero-Montoro, Elena;
Barturen, Guillermo;
Goldman, Daniel;
Petri, Michelle;
Carmona-Sáez, Pedro;
Alarcón-Riquelme, Marta E

Publication type:

Article

NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac338

By:

Zheng, Kai;
Zhao, Haochen;
Zhao, Qichang;
Wang, Bin;
Gao, Xin;
Wang, Jianxin

Publication type:

Article

Clover: tree structure-based efficient DNA clustering for DNA-based data storage.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac336

By:

Qu, Guanjin;
Yan, Zihui;
Wu, Huaming

Publication type:

Article

CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac335

By:

Zhang, Tianjiao;
Jia, Yuran;
Li, Hongfei;
Xu, Dali;
Zhou, Jie;
Wang, Guohua

Publication type:

Article

Performance evaluation of computational methods for splice-disrupting variants and improving the performance using the machine learning-based framework.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac334

By:

Liu, Hao;
Dai, Jiaqi;
Li, Ke;
Sun, Yang;
Wei, Haoran;
Wang, Hong;
Zhao, Chunxia;
Wang, Dao Wen

Publication type:

Article

MGEGFP: a multi-view graph embedding method for gene function prediction based on adaptive estimation with GCN.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac333

By:

Li, Wei;
Zhang, Han;
Li, Minghe;
Han, Mingjing;
Yin, Yanbin

Publication type:

Article

toxCSM: comprehensive prediction of small molecule toxicity profiles.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac337

By:

Sá, Alex G C de;
Long, Yangyang;
Portelli, Stephanie;
Pires, Douglas E V;
Ascher, David B

Publication type:

Article

Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac331

By:

Shen, Xiaotao;
Shao, Wei;
Wang, Chuchu;
Liang, Liang;
Chen, Songjie;
Zhang, Sai;
Rusu, Mirabela;
Snyder, Michael P

Publication type:

Article

Studying protein–protein interaction through side-chain modeling method OPUS-Mut.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac330

By:

Xu, Gang;
Wang, Yilin;
Wang, Qinghua;
Ma, Jianpeng

Publication type:

Article

GREAP: a comprehensive enrichment analysis software for human genomic regions.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac329

By:

Yang, Yongsan;
Qian, Fengcui;
Li, Xuecang;
Li, Yanyu;
Zhou, Liwei;
Wang, Qiuyu;
Zhou, Xinyuan;
Zhang, Jian;
Song, Chao;
Yu, Zhengmin;
Cui, Ting;
Feng, Chenchen;
Zhu, Jiang;
Shang, Desi;
Liu, Jiaqi;
Sun, Mengfei;
Zhang, Yuexin;
Tang, Huifang;
Li, Chunquan

Publication type:

Article

Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac328

By:

Boyraz, Aslı;
Pawlowsky-Glahn, Vera;
Egozcue, Juan José;
Acar, Aybar Can

Publication type:

Article