Works matching IS 14675463 AND DT 2024 AND VI 25 AND IP 2

Results: 129

DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae113

By:

Zhang, Ziying;
Cai, Yaxian;
Zhang, Biao;
Zheng, Wei;
Freddolino, Lydia;
Zhang, Guijun;
Zhou, Xiaogen

Publication type:

Article

Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae110

By:

Han, Dongmei;
Li, Yurun;
Wang, Linxiao;
Liang, Xuan;
Miao, Yuanyuan;
Li, Wenran;
Wang, Sijia;
Wang, Zhen

Publication type:

Article

Correction to: A benchmark study on current GWAS models in admixed populations.

Published in:: 2024
Publication type:: Correction Notice

DDK-Linker: a network-based strategy identifies disease signals by linking high-throughput omics datasets to disease knowledge.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae111

By:

Kong, Xiangren;
Diao, Lihong;
Jiang, Peng;
Nie, Shiyan;
Guo, Shuzhen;
Li, Dong

Publication type:

Article

pathMap: a path-based mapping tool for long noisy reads with high sensitivity.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae107

By:

Wei, Ze-Gang;
Zhang, Xiao-Dan;
Fan, Xing-Guo;
Qian, Yu;
Liu, Fei;
Wu, Fang-Xiang

Publication type:

Article

polyGBLUP: a modified genomic best linear unbiased prediction improved the genomic prediction efficiency for autopolyploid species.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae106

By:

Song, Hailiang;
Zhang, Qin;
Hu, Hongxia

Publication type:

Article

GPCR-IPL score: multilevel featurization of GPCR–ligand interaction patterns and prediction of ligand functions from selectivity to biased activation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae105

By:

Kumar, Surendra;
Teli, Mahesh K;
Kim, Mi-hyun

Publication type:

Article

ReHoGCNES-MDA: prediction of miRNA-disease associations using homogenous graph convolutional networks based on regular graph with random edge sampler.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae103

By:

Zhang, Yufang;
Chu, Yanyi;
Lin, Shenggeng;
Xiong, Yi;
Wei, Dong-Qing

Publication type:

Article

Effective multi-modal clustering method via skip aggregation network for parallel scRNA-seq and scATAC-seq data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae102

By:

Hu, Dayu;
Liang, Ke;
Dong, Zhibin;
Wang, Jun;
Zhao, Yawei;
He, Kunlun

Publication type:

Article

scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae101

By:

Chen, Yuxuan;
Zheng, Ruiqing;
Liu, Jin;
Li, Min

Publication type:

Article

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

Published in:: 2024
Publication type:: Correction Notice

Correction to: Privacy-aware estimation of relatedness in admixed populations.

Published in:: 2024
Publication type:: Correction Notice

The rise of taxon-specific epitope predictors.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae092

By:

Campelo, Felipe;
Lobo, Francisco P

Publication type:

Article

scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae091

By:

Xu, Fei;
Hu, Huan;
Lin, Hai;
Lu, Jun;
Cheng, Feng;
Zhang, Jiqian;
Li, Xiang;
Shuai, Jianwei

Publication type:

Article

Translational bioinformatics and data science for biomarker discovery in mental health: an analytical review.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae098

By:

Bhuvaneshwar, Krithika;
Gusev, Yuriy

Publication type:

Article

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae095

By:

Xiao, Chuxi;
Chen, Yixin;
Meng, Qiuchen;
Wei, Lei;
Zhang, Xuegong

Publication type:

Article

DeTox: a pipeline for the detection of toxins in venomous organisms.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae094

By:

Ringeval, Allan;
Farhat, Sarah;
Fedosov, Alexander;
Gerdol, Marco;
Greco, Samuele;
Mary, Lou;
Modica, Maria Vittoria;
Puillandre, Nicolas

Publication type:

Article

Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae093

By:

Yu, Jiating;
Leng, Jiacheng;
Hou, Zhichao;
Sun, Duanchen;
Wu, Ling-Yun

Publication type:

Article

FusionNW, a potential clinical impact assessment of kinases in pan-cancer fusion gene network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae097

By:

Yang, Chengyuan;
Kumar, Himansu;
Kim, Pora

Publication type:

Article

scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae096

By:

Duan, Ziheng;
Xu, Siwei;
Srinivasan, Shushrruth Sai;
Hwang, Ahyeon;
Lee, Che Yu;
Yue, Feng;
Gerstein, Mark;
Luan, Yu;
Girgenti, Matthew;
Zhang, Jing

Publication type:

Article

High-throughput prediction of enzyme promiscuity based on substrate–product pairs.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae089

By:

Xing, Huadong;
Cai, Pengli;
Liu, Dongliang;
Han, Mengying;
Liu, Juan;
Le, Yingying;
Zhang, Dachuan;
Hu, Qian-Nan

Publication type:

Article

PANCDR: precise medicine prediction using an adversarial network for cancer drug response.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae088

By:

Kim, Juyeon;
Park, Sung-Hye;
Lee, Hyunju

Publication type:

Article

MRSL: a causal network pruning algorithm based on GWAS summary data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae086

By:

Hou, Lei;
Geng, Zhi;
Yuan, Zhongshang;
Shi, Xu;
Wang, Chuan;
Chen, Feng;
Li, Hongkai;
Xue, Fuzhong

Publication type:

Article

MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae087

By:

Shahbazy, Mohammad;
Ramarathinam, Sri H;
Li, Chen;
Illing, Patricia T;
Faridi, Pouya;
Croft, Nathan P;
Purcell, Anthony W

Publication type:

Article

metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae085

By:

Wu, Shufang;
Feng, Tao;
Tang, Waijiao;
Qi, Cancan;
Gao, Jie;
He, Xiaolong;
Wang, Jiaxuan;
Zhou, Hongwei;
Fang, Zhencheng

Publication type:

Article

Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae084

By:

Israeli, Sapir;
Louzoun, Yoram

Publication type:

Article

Enhancer-MDLF: a novel deep learning framework for identifying cell-specific enhancers.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae083

By:

Zhang, Yao;
Zhang, Pengyu;
Wu, Hao

Publication type:

Article

Deep learning in spatially resolved transcriptfomics: a comprehensive technical view.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae082

By:

Zahedi, Roxana;
Ghamsari, Reza;
Argha, Ahmadreza;
Macphillamy, Callum;
Beheshti, Amin;
Alizadehsani, Roohallah;
Lovell, Nigel H;
Lotfollahi, Mohammad;
Alinejad-Rokny, Hamid

Publication type:

Article

Prediction of protein–ligand binding affinity via deep learning models.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae081

By:

Wang, Huiwen

Publication type:

Article

A novel approach to study multi-domain motions in JAK1's activation mechanism based on energy landscape.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae079

By:

Sun, Shengjie;
Rodriguez, Georgialina;
Zhao, Gaoshu;
Sanchez, Jason E;
Guo, Wenhan;
Du, Dan;
Moncivais, Omar J Rodriguez;
Hu, Dehua;
Liu, Jing;
Kirken, Robert Arthur;
Li, Lin

Publication type:

Article

Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae078

By:

Wang, Rui;
Wang, Tao;
Zhuo, Linlin;
Wei, Jinhang;
Fu, Xiangzheng;
Zou, Quan;
Yao, Xiaojun

Publication type:

Article

Deep reinforcement learning identifies personalized intermittent androgen deprivation therapy for prostate cancer.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae071

By:

Lu, Yitao;
Chu, Qian;
Li, Zhen;
Wang, Mengdi;
Gatenby, Robert;
Zhang, Qingpeng

Publication type:

Article

Partial order relation–based gene ontology embedding improves protein function prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae077

By:

Li, Wenjing;
Wang, Bin;
Dai, Jin;
Kou, Yan;
Chen, Xiaojun;
Pan, Yi;
Hu, Shuangwei;
Xu, Zhenjiang Zech

Publication type:

Article

Cracking the black box of deep sequence-based protein–protein interaction prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae076

By:

Bernett, Judith;
Blumenthal, David B;
List, Markus

Publication type:

Article

Ovarian cancer is detectable from peripheral blood using machine learning over T-cell receptor repertoires.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae075

By:

Zuckerbrot-Schuldenfrei, Miriam;
Aviel-Ronen, Sarit;
Zilberberg, Alona;
Efroni, Sol

Publication type:

Article

Correction to: labelSeg: segment annotation for tumor copy number alteration profiles.

Published in:: 2024
Publication type:: Correction Notice

scDOT: enhancing single-cell RNA-Seq data annotation and uncovering novel cell types through multi-reference integration.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae072

By:

Xiong, Yi-Xuan;
Zhang, Xiao-Fei

Publication type:

Article

New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae074

By:

Mokhtari, Majid;
Khoshbakht, Samane;
Ziyaei, Kobra;
Akbari, Mohammad Esmaeil;
Moravveji, Sayyed Sajjad

Publication type:

Article

Enhanced polygenic risk score incorporating gene–environment interaction suggests the association of major depressive disorder with cardiac and lung function.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae070

By:

Pan, Chuyu;
Cheng, Bolun;
Qin, Xiaoyue;
Cheng, Shiqiang;
Liu, Li;
Yang, Xuena;
Meng, Peilin;
Zhang, Na;
He, Dan;
Cai, Qingqing;
Wei, Wenming;
Hui, Jingni;
Wen, Yan;
Jia, Yumeng;
Liu, Huan;
Zhang, Feng

Publication type:

Article

Benchmarking enrichment analysis methods with the disease pathway network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae069

By:

Buzzao, Davide;
Castresana-Aguirre, Miguel;
Guala, Dimitri;
Sonnhammer, Erik L L

Publication type:

Article

scAMAC: self-supervised clustering of scRNA-seq data based on adaptive multi-scale autoencoder.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae068

By:

Tan, Dayu;
Yang, Cheng;
Wang, Jing;
Su, Yansen;
Zheng, Chunhou

Publication type:

Article

Dual-channel hypergraph convolutional network for predicting herb–disease associations.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae067

By:

Hu, Lun;
Zhang, Menglong;
Hu, Pengwei;
Zhang, Jun;
Niu, Chao;
Lu, Xueying;
Jiang, Xiangrui;
Ma, Yupeng

Publication type:

Article

CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae066

By:

Yang, Zitian;
Zhang, Zexin;
Li, Jing;
Chen, Wen;
Liu, Changning

Publication type:

Article

Elevated incidence of somatic mutations at prevalent genetic sites.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae065

By:

Wang, Mengyao;
Li, Shuai Cheng;
Shen, Bairong

Publication type:

Article

RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae064

By:

Bernard, Clement;
Postic, Guillaume;
Ghannay, Sahar;
Tahi, Fariza

Publication type:

Article

Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae063

By:

Wang, Lanying;
Hu, Yuxuan;
Gao, Lin

Publication type:

Article

Correction to: JCcirc: circRNA full-length sequence assembly through integrated junction contigs.

Published in:: 2024
Publication type:: Correction Notice

Exploring miRNA–target gene pair detection in disease with coRmiT.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae060

By:

Cordoba-Caballero, Jose;
Perkins, James R;
García-Criado, Federico;
Gallego, Diana;
Navarro-Sánchez, Alicia;
Moreno-Estellés, Mireia;
Garcés, Concepción;
Bonet, Fernando;
Romá-Mateo, Carlos;
Toro, Rocio;
Perez, Belén;
Sanz, Pascual;
Kohl, Matthias;
Rojano, Elena;
Seoane, Pedro;
Ranea, Juan A G

Publication type:

Article

Deeply integrating latent consistent representations in high-noise multi-omics data for cancer subtyping.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae061

By:

Cai, Yueyi;
Wang, Shunfang

Publication type:

Article

High-dimensional generalized median adaptive lasso with application to omics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae059

By:

Liu, Yahang;
Gao, Qian;
Wei, Kecheng;
Huang, Chen;
Wang, Ce;
Yu, Yongfu;
Qin, Guoyou;
Wang, Tong

Publication type:

Article