Works matching IS 14675463 AND DT 2024 AND VI 25 AND IP 6

Results: 135

A metagene based similarity network fusion approach for multi-omics data integration identified novel subtypes in renal cell carcinoma.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae606

By:

Jia, Congcong;
Wang, Tong;
Cui, Dingtong;
Tian, Yaxin;
Liu, Gaiqin;
Xu, Zhaoyang;
Luo, Yanhong;
Fang, Ruiling;
Yu, Hongmei;
Zhang, Yanbo;
Cui, Yuehua;
Cao, Hongyan

Publication type:

Article

Correction to: Structure prediction of linear and cyclic peptides using CABS-flex.

Published in:: 2024
Publication type:: Correction Notice

SIngle cell level Genotyping Using scRna Data (SIGURD).

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae604

By:

Grasshoff, Martin;
Kalmer, Milena;
Chatain, Nicolas;
Kricheldorf, Kim;
Maurer, Angela;
Weiskirchen, Ralf;
Koschmieder, Steffen;
Costa, Ivan G

Publication type:

Article

The mathematical exploration for the mechanism of lung adenocarcinoma formation and progression.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae603

By:

Han, Yourui;
Chen, Bolin;
Bi, Zhongwen;
Bian, Jun;
Kang, Ruiming;
Shang, Xuequn

Publication type:

Article

Nmix: a hybrid deep learning model for precise prediction of 2'-O-methylation sites based on multi-feature fusion and ensemble learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae601

By:

Geng, Yu-Qing;
Lai, Fei-Liao;
Luo, Hao;
Gao, Feng

Publication type:

Article

Digital annealing optimization for natural product structure elucidation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae600

By:

Lee, Chien;
Wang, Pei-Hua;
Tseng, Yufeng Jane

Publication type:

Article

RiceSNP-BST: a deep learning framework for predicting biotic stress–associated SNPs in rice.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae599

By:

Xu, Jiajun;
Gao, Yujia;
Lu, Quan;
Zhang, Renyi;
Gui, Jianfeng;
Liu, Xiaoshuang;
Yue, Zhenyu

Publication type:

Article

MPA-MutPred: a novel strategy for accurately predicting the binding affinity change upon mutation in membrane protein complexes.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae598

By:

Ridha, Fathima;
Gromiha, M Michael

Publication type:

Article

MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae597

By:

Bosilj, Martin;
Suljič, Alen;
Zakotnik, Samo;
Slunečko, Jan;
Kogoj, Rok;
Korva, Misa

Publication type:

Article

Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae596

By:

Dai, Qi;
Chen, Hu;
Yi, Wen-Jing;
Zhao, Jia-Ning;
Zhang, Wei;
He, Ping-An;
Liu, Xiao-Qing;
Zheng, Ying-Feng;
Shi, Zhuo-Xing

Publication type:

Article

BFAST: joint dimension reduction and spatial clustering with Bayesian factor analysis for zero-inflated spatial transcriptomics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae594

By:

Xu, Yang;
Lv, Dian;
Zou, Xuanxuan;
Wu, Liang;
Xu, Xun;
Zhao, Xin

Publication type:

Article

Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae592

By:

Su, Chen;
Pastor, William A;
Emad, Amin

Publication type:

Article

CMTT-JTracker: a fully test-time adaptive framework serving automated cell lineage construction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae591

By:

Chen, Liuyin;
Fu, Sanyuan;
Zhang, Zijun

Publication type:

Article

Deciphering gene expression patterns using large-scale transcriptomic data and its applications.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae590

By:

Chen, Shunjie;
Wang, Pei;
Guo, Haiping;
Zhang, Yujie

Publication type:

Article

A gentle introduction to pangenomics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae588

By:

Matthews, Chelsea A;
Watson-Haigh, Nathan S;
Burton, Rachel A;
Sheppard, Anna E

Publication type:

Article

TIPS: a novel pathway-guided joint model for transcriptome-wide association studies.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae587

By:

Wang, Neng;
Ye, Zhenyao;
Ma, Tianzhou

Publication type:

Article

Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae586

By:

Park, Sejin;
Lee, Hyunju

Publication type:

Article

SpaGIC: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae578

By:

Liu, Wei;
Wang, Bo;
Bai, Yuting;
Liang, Xiao;
Xue, Li;
Luo, Jiawei

Publication type:

Article

Molecular group and correlation guided structural learning for multi-phenotype prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae585

By:

Zhou, Xueping;
Cai, Manqi;
Yue, Molin;
Celedón, Juan C;
Wang, Jiebiao;
Ding, Ying;
Chen, Wei;
Li, Yanming

Publication type:

Article

ToxGIN: an In silico prediction model for peptide toxicity via graph isomorphism networks integrating peptide sequence and structure information.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae583

By:

Yu, Qiule;
Zhang, Zhixing;
Liu, Guixia;
Li, Weihua;
Tang, Yun

Publication type:

Article

Unlocking cross-modal interplay of single-cell joint profiling with CellMATE.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae582

By:

Wang, Qi;
Zhang, Bolei;
Guo, Yue;
Gong, Luyu;
Li, Erguang;
Yang, Jingping

Publication type:

Article

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae581

By:

Farias, André Borges;
Martinez, Gustavo Sganzerla;
Galán-Vásquez, Edgardo;
Nicolás, Marisa Fabiana;
Pérez-Rueda, Ernesto

Publication type:

Article

mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae580

By:

Tan, Xiaoxiu;
Xue, Feng;
Zhang, Chenhong;
Wang, Tao

Publication type:

Article

Adversarial regularized autoencoder graph neural network for microbe-disease associations prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae584

By:

He, Limuxuan;
Zou, Quan;
Dai, Qi;
Cheng, Shuang;
Wang, Yansu

Publication type:

Article

scTCA: a hybrid Transformer-CNN architecture for imputation and denoising of scDNA-seq data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae577

By:

Yu, Zhenhua;
Liu, Furui;
Li, Yang

Publication type:

Article

Graph domain adaptation–based framework for gene expression enhancement and cell type identification in large-scale spatially resolved transcriptomics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae576

By:

Shen, Rongbo;
Cheng, Meiling;
Wang, Wencang;
Fan, Qi;
Yan, Huan;
Wen, Jiayue;
Yuan, Zhiyuan;
Yao, Jianhua;
Li, Yixue;
Yuan, Jiao

Publication type:

Article

A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae575

By:

Wang, Xin-Fei;
Huang, Lan;
Wang, Yan;
Guan, Ren-Chu;
You, Zhu-Hong;
Sheng, Nan;
Xie, Xu-Ping;
Yang, Qi-Xing

Publication type:

Article

Generating pregnant patient biological profiles by deconvoluting clinical records with electronic health record foundation models.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae574

By:

Seong, David;
Mataraso, Samson;
Espinosa, Camilo;
Berson, Eloise;
Reincke, S Momsen;
Xue, Lei;
Kashiwagi, Chloe;
Kim, Yeasul;
Shu, Chi-Hung;
Chung, Philip;
Ghanem, Marc;
Xie, Feng;
Wong, Ronald J;
Angst, Martin S;
Gaudilliere, Brice;
Shaw, Gary M;
Stevenson, David K;
Aghaeepour, Nima

Publication type:

Article

A multi-task prediction method based on neighborhood structure embedding and signed graph representation learning to infer the relationship between circRNA, miRNA, and cancer.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae573

By:

Huang, Lan;
Wang, Xin-Fei;
Wang, Yan;
Guan, Ren-Chu;
Sheng, Nan;
Xie, Xu-Ping;
Wang, Lei;
Zhao, Zi-qi

Publication type:

Article

Identifying cell types by lasso-constraint regularized Gaussian graphical model based on weighted distance penalty.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae572

By:

Zhang, Wei;
Xu, Yaxin;
Zheng, Xiaoying;
Shen, Juan;
Li, Yuanyuan

Publication type:

Article

SpaDiT: diffusion transformer for spatial gene expression prediction using scRNA-seq.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae571

By:

Li, Xiaoyu;
Zhu, Fangfang;
Min, Wenwen

Publication type:

Article

Making PBPK models more reproducible in practice.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae569

By:

Domínguez-Romero, Elena;
Mazurenko, Stanislav;
Scheringer, Martin;
Santos, Vítor A P Martins dos;
Evelo, Chris T;
Anton, Mihail;
Hancock, John M;
Županič, Anže;
Suarez-Diez, Maria

Publication type:

Article

Deep learning model for protein multi-label subcellular localization and function prediction based on multi-task collaborative training.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae568

By:

Bai, Peihao;
Li, Guanghui;
Luo, Jiawei;
Liang, Cheng

Publication type:

Article

Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae567

By:

Landtsheer, Sébastien De;
Badkas, Apurva;
Kulms, Dagmar;
Sauter, Thomas

Publication type:

Article

AIGen: an artificial intelligence software for complex genetic data analysis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae566

By:

Hou, Tingting;
Shen, Xiaoxi;
Zhang, Shan;
Liang, Muxuan;
Chen, Li;
Lu, Qing

Publication type:

Article

Prototype-based contrastive substructure identification for molecular property prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae565

By:

He, Gaoqi;
Liu, Shun;
Liu, Zhuoran;
Wang, Changbo;
Zhang, Kai;
Li, Honglin

Publication type:

Article

DEWNA: dynamic entropy weight network analysis and its application to the DNA-binding proteome in A549 cells with cisplatin-induced damage.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae564

By:

Wang, Shisheng;
Zeng, Wenjuan;
Yang, Yin;
Cheng, Jingqiu;
Liu, Dan;
Yang, Hao

Publication type:

Article

siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae563

By:

Long, Rongzhuo;
Guo, Ziyu;
Han, Da;
Liu, Boxiang;
Yuan, Xudong;
Chen, Guangyong;
Heng, Pheng-Ann;
Zhang, Liang

Publication type:

Article

Multi-level multi-view network based on structural contrastive learning for scRNA-seq data clustering.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae562

By:

Shu, Zhenqiu;
Xia, Min;
Tan, Kaiwen;
Zhang, Yongbing;
Yu, Zhengtao

Publication type:

Article

Graph databases in systems biology: a systematic review.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae561

By:

Mazein, Ilya;
Rougny, Adrien;
Mazein, Alexander;
Henkel, Ron;
Gütebier, Lea;
Michaelis, Lea;
Ostaszewski, Marek;
Schneider, Reinhard;
Satagopam, Venkata;
Jensen, Lars Juhl;
Waltemath, Dagmar;
Wodke, Judith A H;
Balaur, Irina

Publication type:

Article

Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae560

By:

Phan, Han;
Brouard, Céline;
Mourad, Raphaël

Publication type:

Article

GGN-GO: geometric graph networks for predicting protein function by multi-scale structure features.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae559

By:

Mi, Jia;
Wang, Han;
Li, Jing;
Sun, Jinghong;
Li, Chang;
Wan, Jing;
Zeng, Yuan;
Gao, Jingyang

Publication type:

Article

Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae558

By:

Zhang, Zhenhao;
Liu, Yuxi;
Xiao, Meichen;
Wang, Kun;
Huang, Yu;
Bian, Jiang;
Yang, Ruolin;
Li, Fuyi

Publication type:

Article

A consensus-based classification workflow to determine genetically inferred ancestry from comprehensive genomic profiling of patients with solid tumors.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae557

By:

Wallen, Zachary D;
Nesline, Mary K;
Pabla, Sarabjot;
Gao, Shuang;
Vanroey, Erik;
Hastings, Stephanie B;
Ko, Heidi;
Strickland, Kyle C;
Previs, Rebecca A;
Zhang, Shengle;
Conroy, Jeffrey M;
Jensen, Taylor J;
George, Elizabeth;
Eisenberg, Marcia;
Caveney, Brian;
Sathyan, Pratheesh;
Ramkissoon, Shakti;
Severson, Eric A

Publication type:

Article

An unbiased comparison of immunoglobulin sequence aligners.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae556

By:

Konstantinovsky, Thomas;
Peres, Ayelet;
Polak, Pazit;
Yaari, Gur

Publication type:

Article

scDTL: enhancing single-cell RNA-seq imputation through deep transfer learning with bulk cell information.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae555

By:

Zhao, Liuyang;
Jiang, Landu;
Xie, Yufeng;
Huang, JianHao;
Xie, Haoran;
Tian, Jun;
Zhang, Dian

Publication type:

Article

STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae553

By:

Ran, Peng;
Wang, Yunzhi;
Li, Kai;
He, Shiman;
Tan, Subei;
Lv, Jiacheng;
Zhu, Jiajun;
Tang, Shaoshuai;
Feng, Jinwen;
Qin, Zhaoyu;
Li, Yan;
Huang, Lin;
Yin, Yanan;
Zhu, Lingli;
Yang, Wenjun;
Ding, Chen

Publication type:

Article

IMGT/RobustpMHC: robust training for class-I MHC peptide binding prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae552

By:

Kushwaha, Anjana;
Duroux, Patrice;
Giudicelli, Véronique;
Todorov, Konstantin;
Kossida, Sofia

Publication type:

Article

Multimodal contrastive learning for spatial gene expression prediction using histology images.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae551

By:

Min, Wenwen;
Shi, Zhiceng;
Zhang, Jun;
Wan, Jun;
Wang, Changmiao

Publication type:

Article

Predicting disease-associated microbes based on similarity fusion and deep learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae550

By:

Chen, Hailin;
Chen, Kuan

Publication type:

Article