Works matching IS 14675463 AND DT 2023 AND VI 24 AND IP 6

Results: 90

RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad403

By:

Jiang, Yue;
Hu, Xuejiao;
Fan, Shu;
Liu, Weijiang;
Chen, Jingjing;
Wang, Liang;
Deng, Qianyun;
Yang, Jing;
Yang, Aimei;
Lou, Zheng;
Guan, Yuanlin;
Xia, Han;
Gu, Bing

Publication type:

Article

Rare variant association on unrelated individuals in case–control studies using aggregation tests: existing methods and current limitations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad412

By:

Boutry, Simon;
Helaers, Raphaël;
Lenaerts, Tom;
Vikkula, Miikka

Publication type:

Article

Application of deep learning in cancer epigenetics through DNA methylation analysis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad411

By:

Yassi, Maryam;
Chatterjee, Aniruddha;
Parry, Matthew

Publication type:

Article

PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad418

By:

Yeganeh, Pourya Naderi;
Teo, Yue Y;
Karagkouni, Dimitra;
Pita-Juárez, Yered;
Morgan, Sarah L;
Slack, Frank J;
Vlachos, Ioannis S;
Hide, Winston A

Publication type:

Article

Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad414

By:

Mao, Guo;
Pang, Zhengbin;
Zuo, Ke;
Wang, Qinglin;
Pei, Xiangdong;
Chen, Xinhai;
Liu, Jie

Publication type:

Article

'Artificial intelligence and machine learning in RNA biology'.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad415

By:

Zarnack, Kathi;
Eyras, Eduardo

Publication type:

Article

Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad413

By:

Ketteler, Anna;
Blumenthal, David B

Publication type:

Article

Correction to: CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.

Published in:: 2023
Publication type:: Correction Notice

A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad410

By:

Hu, Xiaowen;
Liu, Dayun;
Zhang, Jiaxuan;
Fan, Yanhao;
Ouyang, Tianxiang;
Luo, Yue;
Zhang, Yuanpeng;
Deng, Lei

Publication type:

Article

Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad405

By:

Dai, Xin;
Wu, Longlong;
Yoo, Shinjae;
Liu, Qun

Publication type:

Article

A prediction model for blood-brain barrier penetrating peptides based on masked peptide transformers with dynamic routing.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad399

By:

Ma, Chunwei;
Wolfinger, Russ

Publication type:

Article

Efficient prediction of peptide self-assembly through sequential and graphical encoding.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad409

By:

Liu, Zihan;
Wang, Jiaqi;
Luo, Yun;
Zhao, Shuang;
Li, Wenbin;
Li, Stan Z

Publication type:

Article

PhaGenus: genus-level classification of bacteriophages using a Transformer model.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad408

By:

Guan, Jiaojiao;
Peng, Cheng;
Shang, Jiayu;
Tang, Xubo;
Sun, Yanni

Publication type:

Article

SMG: self-supervised masked graph learning for cancer gene identification.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad406

By:

Cui, Yan;
Wang, Zhikang;
Wang, Xiaoyu;
Zhang, Yiwen;
Zhang, Ying;
Pan, Tong;
Zhang, Zhe;
Li, Shanshan;
Guo, Yuming;
Akutsu, Tatsuya;
Song, Jiangning

Publication type:

Article

Benchmarking of local genetic correlation estimation methods using summary statistics from genome-wide association studies.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad407

By:

Zhang, Chi;
Zhang, Yiliang;
Zhang, Yunxuan;
Zhao, Hongyu

Publication type:

Article

FG-BERT: a generalized and self-supervised functional group-based molecular representation learning framework for properties prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad398

By:

Li, Biaoshun;
Lin, Mujie;
Chen, Tiegen;
Wang, Ling

Publication type:

Article

DMFDDI: deep multimodal fusion for drug–drug interaction prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad397

By:

Gan, Yanglan;
Liu, Wenxiao;
Xu, Guangwei;
Yan, Cairong;
Zou, Guobing

Publication type:

Article

Chemical structure-aware molecular image representation learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad404

By:

Xiang, Hongxin;
Jin, Shuting;
Liu, Xiangrong;
Zeng, Xiangxiang;
Zeng, Li

Publication type:

Article

KinScan: AI-based rapid profiling of activity across the kinome.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad396

By:

Brahma, Rahul;
Shin, Jae-Min;
Cho, Kwang-Hwi

Publication type:

Article

ConSpaS: a contrastive learning framework for identifying spatial domains by integrating local and global similarities.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad395

By:

Wu, Siyao;
Qiu, Yushan;
Cheng, Xiaoqing

Publication type:

Article

IMOVNN: incomplete multi-omics data integration variational neural networks for gut microbiome disease prediction and biomarker identification.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad394

By:

Hu, Mingyi;
Zhu, Jinlin;
Peng, Guohao;
Lu, Wenwei;
Wang, Hongchao;
Xie, Zhenping

Publication type:

Article

NG-SEM: an effective non-Gaussian structural equation modeling framework for gene regulatory network inference from single-cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad369

By:

Zhao, Jiaying;
Wong, Chi-Wing;
Ching, Wai-Ki;
Cheng, Xiaoqing

Publication type:

Article

scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad391

By:

Li, Wei;
Xiang, Bin;
Yang, Fan;
Rong, Yu;
Yin, Yanbin;
Yao, Jianhua;
Zhang, Han

Publication type:

Article

Breaking the barriers of data scarcity in drug–target affinity prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad386

By:

Pei, Qizhi;
Wu, Lijun;
Zhu, Jinhua;
Xia, Yingce;
Xie, Shufang;
Qin, Tao;
Liu, Haiguang;
Liu, Tie-Yan;
Yan, Rui

Publication type:

Article

MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad393

By:

Liu, Xiaoyi;
Yang, Hongpeng;
Ai, Chengwei;
Ding, Yijie;
Guo, Fei;
Tang, Jijun

Publication type:

Article

Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad370

By:

Shojaee, Abbas;
Huang, Shao-shan Carol

Publication type:

Article

VISN: virus instance segmentation network for TEM images using deep attention transformer.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad373

By:

Xiao, Chi;
Wang, Jun;
Yang, Shenrong;
Heng, Minxin;
Su, Junyi;
Xiao, Hao;
Song, Jingdong;
Li, Weifu

Publication type:

Article

Automated and reproducible cell identification in mass cytometry using neural networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad392

By:

Saihi, Hajar;
Bessant, Conrad;
Alazawi, William

Publication type:

Article

HetDDI: a pre-trained heterogeneous graph neural network model for drug–drug interaction prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad385

By:

Li, Zhe;
Tu, Xinyi;
Chen, Yuping;
Lin, Wenbin

Publication type:

Article

Identifying local associations in biological time series: algorithms, statistical significance, and applications.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad390

By:

Ai, Dongmei;
Chen, Lulu;
Xie, Jiemin;
Cheng, Longwei;
Zhang, Fang;
Luan, Yihui;
Li, Yang;
Hou, Shengwei;
Sun, Fengzhu;
Xia, Li Charlie

Publication type:

Article

FEED: a feature selection method based on gene expression decomposition for single cell clustering.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad389

By:

Zhang, Chao;
Duan, Zhi-Wei;
Xu, Yun-Pei;
Liu, Jin;
Li, Hong-Dong

Publication type:

Article

FLED: a full-length eccDNA detector for long-reads sequencing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad388

By:

Li, Fuyu;
Ming, Wenlong;
Lu, Wenxiang;
Wang, Ying;
Li, Xiaohan;
Dong, Xianjun;
Bai, Yunfei

Publication type:

Article

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad387

By:

Bessell, Brandt;
Loecker, Josh;
Zhao, Zhongyuan;
Aghamiri, Sara Sadat;
Mohanty, Sabyasachi;
Amin, Rada;
Helikar, Tomáš;
Puniya, Bhanwar Lal

Publication type:

Article

Single-cell RNA-sequencing data clustering using variational graph attention auto-encoder with self-supervised leaning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad383

By:

Li, Bo;
Peng, Chen;
You, Zeran;
Zhang, Xiaolong;
Zhang, Shihua

Publication type:

Article

Multiomics dynamic learning enables personalized diagnosis and prognosis for pancancer and cancer subtypes.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad378

By:

Lu, Yuxing;
Peng, Rui;
Dong, Lingkai;
Xia, Kun;
Wu, Renjie;
Xu, Shuai;
Wang, Jinzhuo

Publication type:

Article

scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad384

By:

Wang, Tao;
Zhao, Hui;
Xu, Yungang;
Wang, Yongtian;
Shang, Xuequn;
Peng, Jiajie;
Xiao, Bing

Publication type:

Article

Protein–protein interaction and site prediction using transfer learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad376

By:

Liu, Tuoyu;
Gao, Han;
Ren, Xiaopu;
Xu, Guoshun;
Liu, Bo;
Wu, Ningfeng;
Luo, Huiying;
Wang, Yuan;
Tu, Tao;
Yao, Bin;
Guan, Feifei;
Teng, Yue;
Huang, Huoqing;
Tian, Jian

Publication type:

Article

Filter and Wrapper Stacking Ensemble (FWSE): a robust approach for reliable biomarker discovery in high-dimensional omics data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad382

By:

Budhraja, Sugam;
Doborjeh, Maryam;
Singh, Balkaran;
Tan, Samuel;
Doborjeh, Zohreh;
Lai, Edmund;
Merkin, Alexander;
Lee, Jimmy;
Goh, Wilson;
Kasabov, Nikola

Publication type:

Article

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad381

By:

Seong, Hoon Je;
Kim, Jin Ju;
Sul, Woo Jun

Publication type:

Article

Quantum annealing-based clustering of single cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad377

By:

Kubacki, Michal;
Niranjan, Mahesan

Publication type:

Article

The five pillars of computational reproducibility: bioinformatics and beyond.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad375

By:

Ziemann, Mark;
Poulain, Pierre;
Bora, Anusuiya

Publication type:

Article

Enhancing reinforcement learning for de novo molecular design applying self-attention mechanisms.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad368

By:

Pereira, Tiago O;
Abbasi, Maryam;
Arrais, Joel P

Publication type:

Article

MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad367

By:

Zhang, Quanbao;
Cao, Lei;
Song, Hongtao;
Lin, Kui;
Pang, Erli

Publication type:

Article

CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad374

By:

Su, Qiang;
Long, Yi;
Wang, Jun;
Gou, Deming

Publication type:

Article

SGAE: single-cell gene association entropy for revealing critical states of cell transitions during embryonic development.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad366

By:

Zhong, Jiayuan;
Han, Chongyin;
Chen, Pei;
Liu, Rui

Publication type:

Article

ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad372

By:

Li, Fuyi;
Wang, Cong;
Guo, Xudong;
Akutsu, Tatsuya;
Webb, Geoffrey I;
Coin, Lachlan J M;
Kurgan, Lukasz;
Song, Jiangning

Publication type:

Article

Prediction of multi-relational drug–gene interaction via Dynamic hyperGraph Contrastive Learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad371

By:

Tao, Wen;
Liu, Yuansheng;
Lin, Xuan;
Song, Bosheng;
Zeng, Xiangxiang

Publication type:

Article

Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad335

By:

Lei, Tianyuan;
Chen, Ruoyu;
Zhang, Shaoqiang;
Chen, Yong

Publication type:

Article

OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad365

By:

Xu, Gang;
Luo, Zhenwei;
Zhou, Ruhong;
Wang, Qinghua;
Ma, Jianpeng

Publication type:

Article

Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad351

By:

Adams, Alison K;
Kristy, Brandon D;
Gorman, Myranda;
Balint-Kurti, Peter;
Yencho, G Craig;
Olukolu, Bode A

Publication type:

Article