Works matching IS 14675463 AND DT 2024 AND VI 25 AND IP 1

Results: 106

MHCLMDA: multihypergraph contrastive learning for miRNA–disease association prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad524

By:

Peng, Wei;
He, Zhichen;
Dai, Wei;
Lan, Wei

Publication type:

Article

Correction to: sciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution.

Published in:: 2024
Publication type:: Correction Notice

From data to diagnosis: how machine learning is revolutionizing biomarker discovery in idiopathic inflammatory myopathies.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad514

By:

McLeish, Emily;
Slater, Nataliya;
Mastaglia, Frank L;
Needham, Merrilee;
Coudert, Jerome D

Publication type:

Article

Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad513

By:

Zhang, Ren-Gang;
Shang, Hong-Yun;
Jia, Kai-Hua;
Ma, Yong-Peng

Publication type:

Article

sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad515

By:

Nakatsu, Ken;
Jijiwa, Mayumi;
Khadka, Vedbar;
Nasu, Masaki;
Deng, Youping

Publication type:

Article

Deep neural network learning biological condition information refines gene-expression-based cell subtypes.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad512

By:

Fan, Zhenjiang;
Sun, Jie;
Thorpe, Henry;
Lee, Stephen;
Kim, Soyeon;
Park, Hyun Jung

Publication type:

Article

A granularity-level information fusion strategy on hypergraph transformer for predicting synergistic effects of anticancer drugs.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad522

By:

Wang, Wei;
Yuan, Gaolin;
Wan, Shitong;
Zheng, Ziwei;
Liu, Dong;
Zhang, Hongjun;
Li, Juntao;
Zhou, Yun;
Wang, Xianfang

Publication type:

Article

Accurate identification of structural variations from cancer samples.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad520

By:

Li, Le;
Hong, Chenyang;
Xu, Jie;
Chung, Claire Yik-Lok;
Leung, Alden King-Yung;
Boncan, Delbert Almerick T;
Cheng, Lixin;
Lo, Kwok-Wai;
Lai, Paul B S;
Wong, John;
Zhou, Jingying;
Cheng, Alfred Sze-Lok;
Chan, Ting-Fung;
Yue, Feng;
Yip, Kevin Y

Publication type:

Article

Network pharmacology: towards the artificial intelligence-based precision traditional Chinese medicine.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad518

By:

Zhang, Peng;
Zhang, Dingfan;
Zhou, Wuai;
Wang, Lan;
Wang, Boyang;
Zhang, Tingyu;
Li, Shao

Publication type:

Article

Predicting drug–target binding affinity with cross-scale graph contrastive learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad516

By:

Wang, Jingru;
Xiao, Yihang;
Shang, Xuequn;
Peng, Jiajie

Publication type:

Article

CrossFuse-XGBoost: accurate prediction of the maximum recommended daily dose through multi-feature fusion, cross-validation screening and extreme gradient boosting.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad511

By:

Li, Qiang;
He, Yu;
Pan, Jianbo

Publication type:

Article

Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad509

By:

Shi, Mingyang;
Tanikawa, Chizu;
Munter, Hans Markus;
Akiyama, Masato;
Koyama, Satoshi;
Tomizuka, Kohei;
Matsuda, Koichi;
Lathrop, Gregory Mark;
Terao, Chikashi;
Koido, Masaru;
Kamatani, Yoichiro

Publication type:

Article

scFed: federated learning for cell type classification with scRNA-seq.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad507

By:

Wang, Shuang;
Shen, Bochen;
Guo, Lanting;
Shang, Mengqi;
Liu, Jinze;
Sun, Qi;
Shen, Bairong

Publication type:

Article

DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad506

By:

Qiu, Sizhe;
Zhao, Simiao;
Yang, Aidong

Publication type:

Article

CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad505

By:

Wang, Yizhong;
Li, Yang;
Wang, Cankun;
Lio, Chan-Wang Jerry;
Ma, Qin;
Liu, Bingqiang

Publication type:

Article

SGCAST: symmetric graph convolutional auto-encoder for scalable and accurate study of spatial transcriptomics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad490

By:

Li, Jinzhao;
Wang, Jiong;
Lin, Zhixiang

Publication type:

Article

Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad504

By:

Weber, Jeffrey K;
Morrone, Joseph A;
Kang, Seung-gu;
Zhang, Leili;
Lang, Lijun;
Chowell, Diego;
Krishna, Chirag;
Huynh, Tien;
Parthasarathy, Prerana;
Luan, Binquan;
Alban, Tyler J;
Cornell, Wendy D;
Chan, Timothy A

Publication type:

Article

NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad499

By:

Lin, Yusen;
Zhang, Yongjun;
Sun, Hang;
Jiang, Hang;
Zhao, Xing;
Teng, Xiaojuan;
Lin, Jingxia;
Shu, Bowen;
Sun, Hao;
Liao, Yuhui;
Zhou, Jiajian

Publication type:

Article

A critical assessment of clustering algorithms to improve cell clustering and identification in single-cell transcriptome study.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad497

By:

Liang, Xiao;
Cao, Lijie;
Chen, Hao;
Wang, Lidan;
Wang, Yangyun;
Fu, Lijuan;
Tan, Xiaqin;
Chen, Enxiang;
Ding, Yubin;
Tang, Jing

Publication type:

Article

'Bingo'—a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad472

By:

Ma, Jiani;
Song, Jiangning;
Young, Neil D;
Chang, Bill C H;
Korhonen, Pasi K;
Campos, Tulio L;
Liu, Hui;
Gasser, Robin B

Publication type:

Article

Development of innovative multi-epitope mRNA vaccine against Pseudomonas aeruginosa using in silico approaches.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad502

By:

Asadinezhad, Maryam;
Khoshnood, Saeed;
Asadollahi, Parisa;
Ghafourian, Sobhan;
Sadeghifard, Nourkhoda;
Pakzad, Iraj;
Zeinivand, Yasaman;
Omidi, Nazanin;
Hematian, Ali;
Kalani, Behrooz Sadeghi

Publication type:

Article

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

Published in:: 2024
Publication type:: Correction Notice

Consensus clustering with missing labels (ccml): a consensus clustering tool for multi-omics integrative prediction in cohorts with unequal sample coverage.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad501

By:

Li, Chuan-Xing;
Chen, Hongyan;
Zounemat-Kermani, Nazanin;
Adcock, Ian M;
Sköld, C Magnus;
Zhou, Meng;
Wheelock, Åsa M;
group, U-BIOPRED study

Publication type:

Article

SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad494

By:

Pan, Jian-Hua;
Du, Pu-Feng

Publication type:

Article

stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad500

By:

Fang, Zhaoyu;
Liu, Teng;
Zheng, Ruiqing;
A, Jin;
Yin, Mingzhu;
Li, Min

Publication type:

Article

MrGPS: an m6A-related gene pair signature to predict the prognosis and immunological impact of glioma patients.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad498

By:

Zhang, Ning;
Yang, Fengxia;
Zhao, Pengfei;
Jin, Nana;
Wu, Haonan;
Liu, Tao;
Geng, Qingshan;
Yang, Xiaojun;
Cheng, Lixin

Publication type:

Article

Structural coverage of the human interactome.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad496

By:

Kosoglu, Kayra;
Aydin, Zeynep;
Tuncbag, Nurcan;
Gursoy, Attila;
Keskin, Ozlem

Publication type:

Article

The role of ncRNA regulatory mechanisms in diseases—case on gestational diabetes.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad489

By:

Gao, Dong;
Ren, Liping;
Hao, Yu-Duo;
Schaduangrat, Nalini;
Liu, Xiao-Wei;
Yuan, Shi-Shi;
Yang, Yu-He;
Wang, Yan;
Shoombuatong, Watshara;
Ding, Hui

Publication type:

Article

Protein–DNA binding sites prediction based on pre-trained protein language model and contrastive learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad488

By:

Liu, Yufan;
Tian, Boxue

Publication type:

Article

ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad495

By:

Lee, Jin Seok;
Karthikeyan, Dhuvarakesh;
Fini, Misha;
Vincent, Benjamin G;
Rubinsteyn, Alex

Publication type:

Article

AMGDTI: drug–target interaction prediction based on adaptive meta-graph learning in heterogeneous network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad474

By:

Su, Yansen;
Hu, Zhiyang;
Wang, Fei;
Bin, Yannan;
Zheng, Chunhou;
Li, Haitao;
Chen, Haowen;
Zeng, Xiangxiang

Publication type:

Article

Opportunities and challenges for ChatGPT and large language models in biomedicine and health.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad493

By:

Tian, Shubo;
Jin, Qiao;
Yeganova, Lana;
Lai, Po-Ting;
Zhu, Qingqing;
Chen, Xiuying;
Yang, Yifan;
Chen, Qingyu;
Kim, Won;
Comeau, Donald C;
Islamaj, Rezarta;
Kapoor, Aadit;
Gao, Xin;
Lu, Zhiyong

Publication type:

Article

Identify gestational diabetes mellitus by deep learning model from cell-free DNA at the early gestation stage.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad492

By:

Wang, Yipeng;
Sun, Pei;
Zhao, Zicheng;
Yan, Yousheng;
Yue, Wentao;
Yang, Kai;
Liu, Ruixia;
Huang, Hui;
Wang, Yinan;
Chen, Yin;
Li, Nan;
Feng, Hailong;
Li, Jing;
Liu, Yifan;
Chen, Yujiao;
Shen, Bairong;
Zhao, Lijian;
Yin, Chenghong

Publication type:

Article

Quantification of biases in predictions of protein–protein binding affinity changes upon mutations.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad491

By:

Tsishyn, Matsvei;
Pucci, Fabrizio;
Rooman, Marianne

Publication type:

Article

VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad480

By:

Xu, Xiaofeng;
Li, Ying;
Chen, Taoyu;
Hou, Chao;
Yang, Liang;
Zhu, Peiyu;
Zhang, Yi;
Li, Tingting

Publication type:

Article

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

Published in:: 2024
Publication type:: Correction Notice

Integrated bulk and single-cell transcriptomes reveal pyroptotic signature in prognosis and therapeutic options of hepatocellular carcinoma by combining deep learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad487

By:

Liu, Yang;
Li, Hanlin;
Zeng, Tianyu;
Wang, Yang;
Zhang, Hongqi;
Wan, Ying;
Shi, Zheng;
Cao, Renzhi;
Tang, Hua

Publication type:

Article

Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad486

By:

Wang, Tianyue;
Wang, Langcheng;
Zhang, Xujun;
Shen, Chao;
Zhang, Odin;
Wang, Jike;
Wu, Jialu;
Jin, Ruofan;
Zhou, Donghao;
Chen, Shicheng;
Liu, Liwei;
Wang, Xiaorui;
Hsieh, Chang-Yu;
Chen, Guangyong;
Pan, Peichen;
Kang, Yu;
Hou, Tingjun

Publication type:

Article

methylClass: an R package to construct DNA methylation-based classification models.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad485

By:

Liu, Yu

Publication type:

Article

MulinforCPI: enhancing precision of compound–protein interaction prediction through novel perspectives on multi-level information integration.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad484

By:

Nguyen, Ngoc-Quang;
Park, Sejeong;
Gim, Mogan;
Kang, Jaewoo

Publication type:

Article

Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad483

By:

Zhou, Zhecheng;
Zhuo, Linlin;
Fu, Xiangzheng;
Zou, Quan

Publication type:

Article

Advancing single-cell RNA-seq data analysis through the fusion of multi-layer perceptron and graph neural network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad481

By:

Feng, Xiang;
Xiu, Yu-Han;
Long, Hai-Xia;
Wang, Zi-Tong;
Bilal, Anas;
Yang, Li-Ming

Publication type:

Article

RNet: a network strategy to predict RNA binding preferences.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad482

By:

Liu, Haoquan;
Jian, Yiren;
Hou, Jinxuan;
Zeng, Chen;
Zhao, Yunjie

Publication type:

Article

H2Opred: a robust and efficient hybrid deep learning model for predicting 2'-O-methylation sites in human RNA.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad476

By:

Pham, Nhat Truong;
Rakkiyapan, Rajan;
Park, Jongsun;
Malik, Adeel;
Manavalan, Balachandran

Publication type:

Article

CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad475

By:

Liu, Jin;
Zeng, Weixing;
Kan, Shichao;
Li, Min;
Zheng, Ruiqing

Publication type:

Article

A review of genetic variant databases and machine learning tools for predicting the pathogenicity of breast cancer.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad479

By:

Ahmad, Rahaf M;
Ali, Bassam R;
Al-Jasmi, Fatma;
Sinnott, Richard O;
Dhaheri, Noura Al;
Mohamad, Mohd Saberi

Publication type:

Article

Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad478

By:

Li, Ying;
Gao, Jing;
Zheng, Xubin;
Nie, Guole;
Qin, Jican;
Wang, Haiping;
He, Tao;
Wheelock, Åsa;
Li, Chuan-Xing;
Cheng, Lixin;
Li, Xun

Publication type:

Article

MMP<sup>3</sup>C: an in-silico framework to depict cancer metabolic plasticity using gene expression profiles.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad471

By:

Chen, Xingyu;
Deng, Min;
Wang, Zihan;
Huang, Chen

Publication type:

Article

Applying polygenic risk score methods to pharmacogenomics GWAS: challenges and opportunities.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad470

By:

Zhai, Song;
Mehrotra, Devan V;
Shen, Judong

Publication type:

Article

GTAD: a graph-based approach for cell spatial composition inference from integrated scRNA-seq and ST-seq data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad469

By:

Zhang, Tianjiao;
Zhang, Ziheng;
Li, Liangyu;
Dong, Benzhi;
Wang, Guohua;
Zhang, Dandan

Publication type:

Article