Works matching IS 14675463 AND DT 2024 AND VI 25 AND IP 3

Results: 127

Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Published in:: 2024
Publication type:: Correction Notice

Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae247

By:

Lin, Yicheng;
Ma, Jiakang;
Yuan, Haozhe;
Chen, Ziqiang;
Xu, Xingyu;
Jiang, Mengping;
Zhu, Jialiang;
Meng, Weida;
Qiu, Wenqing;
Liu, Yun

Publication type:

Article

Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae241

By:

Singh, Vikas;
Kirtipal, Nikhil;
Song, Byeongsop;
Lee, Sunjae

Publication type:

Article

A perspective on genetic and polygenic risk scores—advances and limitations and overview of associated tools.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae240

By:

Schwarzerova, Jana;
Hurta, Martin;
Barton, Vojtech;
Lexa, Matej;
Walther, Dirk;
Provaznik, Valentine;
Weckwerth, Wolfram

Publication type:

Article

MSI-DTI: predicting drug-target interaction based on multi-source information and multi-head self-attention.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae238

By:

Zhao, Wenchuan;
Yu, Yufeng;
Liu, Guosheng;
Liang, Yanchun;
Xu, Dong;
Feng, Xiaoyue;
Guan, Renchu

Publication type:

Article

CPADS: a web tool for comprehensive pancancer analysis of drug sensitivity.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae237

By:

Li, Kexin;
Yang, Hong;
Lin, Anqi;
Xie, Jiayi;
Wang, Haitao;
Zhou, Jianguo;
Carr, Shamus R;
Liu, Zaoqu;
Li, Xiaohua;
Zhang, Jian;
Cheng, Quan;
Schrump, David S;
Luo, Peng;
Wei, Ting

Publication type:

Article

Computational deconvolution of DNA methylation data from mixed DNA samples.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae234

By:

Santos, Maísa R Ferro dos;
Giuili, Edoardo;
Koker, Andries De;
Everaert, Celine;
Preter, Katleen De

Publication type:

Article

Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae233

By:

Barra, Jasmine;
Taverna, Federico;
Bong, Fabian;
Ahmed, Ibrahim;
Karakach, Tobias K

Publication type:

Article

SGCLDGA: unveiling drug–gene associations through simple graph contrastive learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae231

By:

Fan, Yanhao;
Zhang, Che;
Hu, Xiaowen;
Huang, Zhijian;
Xue, Jiameng;
Deng, Lei

Publication type:

Article

Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs).

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae230

By:

Alamin, Md;
Sultana, Most Humaira;
Babarinde, Isaac Adeyemi;
Azad, A K M;
Moni, Mohammad Ali;
Xu, Haiming

Publication type:

Article

AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae229

By:

Wei, Xin;
Tan, Huagang;
Lobb, Briallen;
Zhen, William;
Wu, Zijing;
Parks, Donovan H;
Neufeld, Josh D;
Moreno-Hagelsieb, Gabriel;
Doxey, Andrew C

Publication type:

Article

scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae228

By:

Qiu, Yushan;
Guo, Dong;
Zhao, Pu;
Zou, Quan

Publication type:

Article

Optimal fusion of genotype and drug embeddings in predicting cancer drug response.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae227

By:

Nguyen, Trang;
Campbell, Anthony;
Kumar, Ankit;
Amponsah, Edwin;
Fiterau, Madalina;
Shahriyari, Leili

Publication type:

Article

Correction to: A new paradigm for applying deep learning to protein–ligand interaction prediction.

Published in:: 2024
Publication type:: Correction Notice

Analysis of Emerging Variants of Turkey Reovirus using Machine Learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae224

By:

KafiKang, Maryam;
Abeysiriwardana, Chamudi;
Singh, Vikash K;
Koh, Chan Young;
Prichard, Janet;
Mor, Sunil K;
Hendawi, Abdeltawab

Publication type:

Article

FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae223

By:

Zhou, Yuan;
Chen, Zhen;
Yang, Mengjie;
Chen, Fengyun;
Yin, Jiayi;
Zhang, Yintao;
Zhou, Xuheng;
Sun, Xiuna;
Ni, Ziheng;
Chen, Lu;
Lv, Qun;
Zhu, Feng;
Liu, Shuiping

Publication type:

Article

Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae221

By:

Peres, Ayelet;
Klein, Vered;
Frankel, Boaz;
Lees, William;
Polak, Pazit;
Meehan, Mark;
Rocha, Artur;
Lopes, João Correia;
Yaari, Gur

Publication type:

Article

Contrastive learning for enhancing feature extraction in anticancer peptides.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae220

By:

Lee, Byungjo;
Shin, Dongkwan

Publication type:

Article

Towards multi-omics synthetic data integration.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae213

By:

Selvarajoo, Kumar;
Maurer-Stroh, Sebastian

Publication type:

Article

TransPTM: a transformer-based model for non-histone acetylation site prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae219

By:

Meng, Lingkuan;
Chen, Xingjian;
Cheng, Ke;
Chen, Nanjun;
Zheng, Zetian;
Wang, Fuzhou;
Sun, Hongyan;
Wong, Ka-Chun

Publication type:

Article

PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae218

By:

Saha, Gourab;
Sawmya, Shashata;
Saha, Arpita;
Akil, Md Ajwad;
Tasnim, Sadia;
Rahman, Md Saifur;
Rahman, M Sohel

Publication type:

Article

Removing unwanted variation between samples in Hi-C experiments.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae217

By:

Fletez-Brant, Kipper;
Qiu, Yunjiang;
Gorkin, David U;
Hu, Ming;
Hansen, Kasper D

Publication type:

Article

Response to Letter to Editor 'Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine'.

Published in:

2024

By:

Tian, Shubo;
Jin, Qiao;
Lu, Zhiyong

Publication type:

Letter to the Editor

Predicting TCR sequences for unseen antigen epitopes using structural and sequence features.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae210

By:

Ji, Hongchen;
Wang, Xiang-Xu;
Zhang, Qiong;
Zhang, Chengkai;
Zhang, Hong-Mei

Publication type:

Article

Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae216

By:

Dong, Xiaoru;
Leary, Jack R;
Yang, Chuanhao;
Brusko, Maigan A;
Brusko, Todd M;
Bacher, Rhonda

Publication type:

Article

DDID: a comprehensive resource for visualization and analysis of diet–drug interactions.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae212

By:

Hong, Yanfeng;
Xu, Hongquan;
Liu, Yuhong;
Zhu, Sisi;
Tian, Chao;
Chen, Gongxing;
Zhu, Feng;
Tao, Lin

Publication type:

Article

HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae215

By:

Zhang, Chenhao;
Zhang, Chengyun;
Shang, Tianfeng;
Zhu, Ning;
Wu, Xinyi;
Duan, Hongliang

Publication type:

Article

Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae214

By:

Ray, Partha Pratim

Publication type:

Article

Single-cell RNA sequencing data imputation using bi-level feature propagation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae209

By:

Lee, Junseok;
Yun, Sukwon;
Kim, Yeongmin;
Chen, Tianlong;
Kellis, Manolis;
Park, Chanyoung

Publication type:

Article

A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae208

By:

Guan, Jiahui;
Yao, Lantian;
Xie, Peilin;
Chung, Chia-Ru;
Huang, Yixian;
Chiang, Ying-Chih;
Lee, Tzong-Yi

Publication type:

Article

AI identifies potent inducers of breast cancer stem cell differentiation based on adversarial learning from gene expression data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae207

By:

Li, Zhongxiao;
Napolitano, Antonella;
Fedele, Monica;
Gao, Xin;
Napolitano, Francesco

Publication type:

Article

BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae195

By:

Wang, Kai;
Zeng, Xuan;
Zhou, Jingwen;
Liu, Fei;
Luan, Xiaoli;
Wang, Xinglong

Publication type:

Article

Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae206

By:

Hu, Kaixin;
Meyer, Fernando;
Deng, Zhi-Luo;
Asgari, Ehsaneddin;
Kuo, Tzu-Hao;
Münch, Philipp C;
McHardy, Alice C

Publication type:

Article

scCRT: a contrastive-based dimensionality reduction model for scRNA-seq trajectory inference.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae204

By:

Shi, Yuchen;
Wan, Jian;
Zhang, Xin;
Liang, Tingting;
Yin, Yuyu

Publication type:

Article

scEWE: high-order element-wise weighted ensemble clustering for heterogeneity analysis of single-cell RNA-sequencing data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae203

By:

Huang, Yixiang;
Jiang, Hao;
Ching, Wai-Ki

Publication type:

Article

Revealing cell–cell communication pathways with their spatially coupled gene programs.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae202

By:

Zhu, Junchao;
Dai, Hao;
Chen, Luonan

Publication type:

Article

GSScore: a novel Graphormer-based shell-like scoring method for protein–ligand docking.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae201

By:

Guo, Linyuan;
Wang, Jianxin

Publication type:

Article

mbDecoda: a debiased approach to compositional data analysis for microbiome surveys.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae205

By:

Zong, Yuxuan;
Zhao, Hongyu;
Wang, Tao

Publication type:

Article

Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae199

By:

Kishk, Ali;
Pacheco, Maria Pires;
Heurtaux, Tony;
Sauter, Thomas

Publication type:

Article

CPPLS-MLP: a method for constructing cell–cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae198

By:

Zhang, Tianjiao;
Wu, Zhenao;
Li, Liangyu;
Ren, Jixiang;
Zhang, Ziheng;
Wang, Guohua

Publication type:

Article

PanDepth, an ultrafast and efficient genomic tool for coverage calculation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae197

By:

Yu, Huiyang;
Shi, Chunmei;
He, Weiming;
Li, Feng;
Ouyang, Bo

Publication type:

Article

DeepSS2GO: protein function prediction from secondary structure.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae196

By:

Song, Fu V;
Su, Jiaqi;
Huang, Sixing;
Zhang, Neng;
Li, Kaiyue;
Ni, Ming;
Liao, Maofu

Publication type:

Article

TransAC4C—a novel interpretable architecture for multi-species identification of N4-acetylcytidine sites in RNA with single-base resolution.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae200

By:

Liu, Ruijie;
Zhang, Yuanpeng;
Wang, Qi;
Zhang, Xiaoping

Publication type:

Article

DEGAP: Dynamic elongation of a genome assembly path.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae194

By:

Huang, Yicheng;
Wang, Ziyuan;
Schmidt, Monica A;
Su, Handong;
Xiong, Lizhong;
Zhang, Jianwei

Publication type:

Article

SC-Track: a robust cell-tracking algorithm for generating accurate single-cell lineages from diverse cell segmentations.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae192

By:

Li, Chengxin;
Xie, Shuang Shuang;
Wang, Jiaqi;
Sharvia, Septavera;
Chan, Kuan Yoow

Publication type:

Article

Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae193

By:

Yang, Guang;
Li, Jianing;
Hu, Jinlu;
Shi, Jian-Yu

Publication type:

Article

Genotypic–phenotypic landscape computation based on first principle and deep learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae191

By:

Liu, Yuexing;
Luo, Yao;
Lu, Xin;
Gao, Hao;
He, Ruikun;
Zhang, Xin;
Zhang, Xuguang;
Li, Yixue

Publication type:

Article

CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae190

By:

Liu, Lei;
Yang, Liu;
Cao, Suqi;
Gao, Zhigang;
Yang, Bin;
Zhang, Guoqing;
Zhu, Ruixin;
Wu, Dingfeng

Publication type:

Article

SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae189

By:

Wan, Guihong;
Maliga, Zoltan;
Yan, Boshen;
Vallius, Tuulia;
Shi, Yingxiao;
Khattab, Sara;
Chang, Crystal;
Nirmal, Ajit J;
Yu, Kun-Hsing;
Liu, David;
Lian, Christine G;
DeSimone, Mia S;
Sorger, Peter K;
Semenov, Yevgeniy R

Publication type:

Article

scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae188

By:

Zhai, Yuyao;
Chen, Liang;
Deng, Minghua

Publication type:

Article