Works matching IS 14675463 AND DT 2023 AND VI 24 AND IP 3

Results: 87

DiMo: discovery of microRNA motifs using deep learning and motif embedding.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad182

By:

Farhadi, Fatemeh;
Allahbakhsh, Mohammad;
Maghsoudi, Ali;
Armin, Nadieh;
Amintoosi, Haleh

Publication type:

Article

P-CSN: single-cell RNA sequencing data analysis by partial cell-specific network.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad180

By:

Wang, Yan;
Xuan, Chenxu;
Wu, Hanwen;
Zhang, Bai;
Ding, Tao;
Gao, Jie

Publication type:

Article

scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad179

By:

Liu, Hongjia;
Li, Huamei;
Sharma, Amit;
Huang, Wenjuan;
Pan, Duo;
Gu, Yu;
Lin, Lu;
Sun, Xiao;
Liu, Hongde

Publication type:

Article

Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad178

By:

Xu, Wei;
Wang, Teng;
Wang, Nan;
Zhang, Haohong;
Zha, Yuguo;
Ji, Lei;
Chu, Yuwen;
Ning, Kang

Publication type:

Article

Editorial.

Published in:

2023

By:

Bishop, Martin

Publication type:

Editorial

Quantitative annotations of T-Cell repertoire specificity.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad175

By:

Luo, Jiaqi;
Wang, Xueying;
Zou, Yiping;
Chen, Lingxi;
Liu, Wei;
Zhang, Wei;
Li, Shuai Cheng

Publication type:

Article

McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad174

By:

Li, Lun;
Xu, Bo;
Tian, Dongmei;
Wang, Anke;
Zhu, Junwei;
Li, Cuiping;
Li, Na;
Zhao, Wei;
Shi, Leisheng;
Xue, Yongbiao;
Zhang, Zhang;
Bao, Yiming;
Zhao, Wenming;
Song, Shuhui

Publication type:

Article

ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad170

By:

Chen, Ruyi;
Li, Fuyi;
Guo, Xudong;
Bi, Yue;
Li, Chen;
Pan, Shirui;
Coin, Lachlan J M;
Song, Jiangning

Publication type:

Article

SLHSD: hybrid scaffolding method based on short and long reads.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad169

By:

Luo, Junwei;
Guan, Ting;
Chen, Guolin;
Yu, Zhonghua;
Zhai, Haixia;
Yan, Chaokun;
Luo, Huimin

Publication type:

Article

Translational informatics for human microbiota: data resources, models and applications.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad168

By:

Shen, Ke;
Din, Ahmad Ud;
Sinha, Baivab;
Zhou, Yi;
Qian, Fuliang;
Shen, Bairong

Publication type:

Article

KGANSynergy: knowledge graph attention network for drug synergy prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad167

By:

Zhang, Ge;
Gao, Zhijie;
Yan, Chaokun;
Wang, Jianlin;
Liang, Wenjuan;
Luo, Junwei;
Luo, Huimin

Publication type:

Article

InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad166

By:

Zhang, Feng;
Jiao, Huiyuan;
Wang, Yihao;
Yang, Chen;
Li, Linying;
Wang, Zhiming;
Tong, Ran;
Zhou, Junmei;
Shen, Jianfeng;
Li, Lingjie

Publication type:

Article

LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad165

By:

Liu, Jian;
Li, Pingjing;
Sun, Jialiang;
Guo, Jun

Publication type:

Article

STMHCpan, an accurate Star-Transformer-based extensible framework for predicting MHC I allele binding peptides.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad164

By:

Ye, Zheng;
Li, Shaohao;
Mi, Xue;
Shao, Baoyi;
Dai, Zhu;
Ding, Bo;
Feng, Songwei;
Sun, Bo;
Shen, Yang;
Xiao, Zhongdang

Publication type:

Article

Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad163

By:

Mateos, Pablo Acera;
Zhou, You;
Zarnack, Kathi;
Eyras, Eduardo

Publication type:

Article

A survey on computational strategies for genome-resolved gut metagenomics.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad162

By:

Jia, Longhao;
Wu, Yingjian;
Dong, Yanqi;
Chen, Jingchao;
Chen, Wei-Hua;
Zhao, Xing-Ming

Publication type:

Article

Multi-modality attribute learning-based method for drug–protein interaction prediction based on deep neural network.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad161

By:

Dong, Weihe;
Yang, Qiang;
Wang, Jian;
Xu, Long;
Li, Xiaokun;
Luo, Gongning;
Gao, Xin

Publication type:

Article

Leveraging developmental landscapes for model selection in Boolean gene regulatory networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad160

By:

Subbaroyan, Ajay;
Sil, Priyotosh;
Martin, Olivier C;
Samal, Areejit

Publication type:

Article

Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad159

By:

Cao, Yue;
Ghazanfar, Shila;
Yang, Pengyi;
Yang, Jean

Publication type:

Article

MKMR: a multi-kernel machine regression model to predict health outcomes using human microbiome data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad158

By:

Li, Bing;
Wang, Tian;
Qian, Min;
Wang, Shuang

Publication type:

Article

CosTaL: an accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad157

By:

Li, Yijia;
Nguyen, Jonathan;
Anastasiu, David C;
Arriaga, Edgar A

Publication type:

Article

A survey on algorithms to characterize transcription factor binding sites.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad156

By:

Tognon, Manuel;
Giugno, Rosalba;
Pinello, Luca

Publication type:

Article

Computational approaches for circRNAs prediction and in silico characterization.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad154

By:

Rebolledo, Camilo;
Silva, Juan Pablo;
Saavedra, Nicolás;
Maracaja-Coutinho, Vinicius

Publication type:

Article

Machine learning for RNA 2D structure prediction benchmarked on experimental data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad153

By:

Justyna, Marek;
Antczak, Maciej;
Szachniuk, Marta

Publication type:

Article

Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad152

By:

Jiang, Jing;
Xu, Junlin;
Liu, Yuansheng;
Song, Bosheng;
Guo, Xiulan;
Zeng, Xiangxiang;
Zou, Quan

Publication type:

Article

Recent application of artificial intelligence on histopathologic image-based prediction of gene mutation in solid cancers.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad151

By:

Alam, Mohammad Rizwan;
Seo, Kyung Jin;
Abdul-Ghafar, Jamshid;
Yim, Kwangil;
Lee, Sung Hak;
Jang, Hyun-Jong;
Jung, Chan Kwon;
Chong, Yosep

Publication type:

Article

A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad150

By:

Wang, Meng;
Kurgan, Lukasz;
Li, Min

Publication type:

Article

SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad149

By:

Qiu, Yushan;
Yan, Chang;
Zhao, Pu;
Zou, Quan

Publication type:

Article

A strategy combining denoising and cryo-EM single particle analysis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad148

By:

Zhang, Hui;
Li, Hongjia;
Zhang, Fa;
Zhu, Ping

Publication type:

Article

Short human eccDNAs are predictable from sequences.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad147

By:

Chang, Kai-Li;
Chen, Jia-Hong;
Lin, Tzu-Chieh;
Leu, Jun-Yi;
Kao, Cheng-Fu;
Wong, Jin Yung;
Tsai, Huai-Kuang

Publication type:

Article

Graph deep learning enabled spatial domains identification for spatial transcriptomics.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad146

By:

Liu, Teng;
Fang, Zhao-Yu;
Li, Xin;
Zhang, Li-Ning;
Cao, Dong-Sheng;
Yin, Ming-Zhu

Publication type:

Article

Sars-escape network for escape prediction of SARS-COV-2.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad140

By:

Bist, Prem Singh;
Tayara, Hilal;
Chong, Kil To

Publication type:

Article

An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad144

By:

Fang, Kechi;
Li, Chuan;
Wang, Jing

Publication type:

Article

Potential of dissimilarity measure-based computation of protein thermal stability data for determining protein interactions.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad143

By:

Teitz, Joshua;
Sander, Joerg;
Sarker, Hassan;
Fernandez-Patron, Carlos

Publication type:

Article

Decoding Connectivity Map-based drug repurposing for oncotherapy.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad142

By:

Zhao, Yuanchun;
Chen, Xingqi;
Chen, Jiajia;
Qi, Xin

Publication type:

Article

SmartGate is a spatial metabolomics tool for resolving tissue structures.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad141

By:

Xiao, Kaixuan;
Wang, Yu;
Dong, Kangning;
Zhang, Shihua

Publication type:

Article

Improving drug-target affinity prediction via feature fusion and knowledge distillation.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad145

By:

Lu, Ruiqiang;
Wang, Jun;
Li, Pengyong;
Li, Yuquan;
Tan, Shuoyan;
Pan, Yiting;
Liu, Huanxiang;
Gao, Peng;
Xie, Guotong;
Yao, Xiaojun

Publication type:

Article

Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad139

By:

Duan, Daoyu;
Tang, Wen;
Wang, Runshu;
Guo, Zhenxing;
Feng, Hao

Publication type:

Article

Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad138

By:

Chen, Yigang;
Lin, Yang-Chi-Dung;
Luo, Yijun;
Cai, Xiaoxuan;
Qiu, Peng;
Cui, Shidong;
Wang, Zhe;
Huang, Hsi-Yuan;
Huang, Hsien-Da

Publication type:

Article

A novel heterophilic graph diffusion convolutional network for identifying cancer driver genes.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad137

By:

Zhang, Tong;
Zhang, Shao-Wu;
Xie, Ming-Yu;
Li, Yan

Publication type:

Article

BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad136

By:

Yousefi, Niloofar;
Yazdani-Jahromi, Mehdi;
Tayebi, Aida;
Kolanthai, Elayaraja;
Neal, Craig J;
Banerjee, Tanumoy;
Gosai, Agnivo;
Balasubramanian, Ganesh;
Seal, Sudipta;
Garibay, Ozlem Ozmen

Publication type:

Article

UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad135

By:

Du, Zhenjiao;
Ding, Xingjian;
Xu, Yixiang;
Li, Yonghui

Publication type:

Article

Correction to: Quantum computing algorithms: getting closer to critical problems in computational biology.

Published in:: 2023
Publication type:: Correction Notice

Decoding CRISPR–Cas PAM recognition with UniDesign.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad133

By:

Huang, Xiaoqiang;
Zhou, Jun;
Yang, Dongshan;
Zhang, Jifeng;
Xia, Xiaofeng;
Chen, Yuqing Eugene;
Xu, Jie

Publication type:

Article

Transformer-based anti-noise models for CRISPR-Cas9 off-target activities prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad127

By:

Guan, Zengrui;
Jiang, Zhenran

Publication type:

Article

Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad131

By:

Sherkatghanad, Zeinab;
Abdar, Moloud;
Charlier, Jeremy;
Makarenkov, Vladimir

Publication type:

Article

Matching single cells across modalities with contrastive learning and optimal transport.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad130

By:

Gossi, Federico;
Pati, Pushpak;
Chouvardas, Panagiotis;
Martinelli, Adriano Luca;
Julio, Marianna Kruithof-de;
Rapsomaniki, Maria Anna

Publication type:

Article

NSRGRN: a network structure refinement method for gene regulatory network inference.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad129

By:

Liu, Wei;
Yang, Yu;
Lu, Xu;
Fu, Xiangzheng;
Sun, Ruiqing;
Yang, Li;
Peng, Li

Publication type:

Article

Correction to: Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design.

Published in:: Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad128
Publication type:: Article

TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad132

By:

Liu, Yan;
Wei, Guo;
Li, Chen;
Shen, Long-Chen;
Gasser, Robin B;
Song, Jiangning;
Chen, Dijun;
Yu, Dong-Jun

Publication type:

Article