Works matching IS 14675463 AND DT 2025 AND VI 26 AND IP 1

Results: 196

Correction to: Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison.

Published in:: 2025
Publication type:: Correction Notice

NP-TCMtarget: a network pharmacology platform for exploring mechanisms of action of traditional Chinese medicine.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf078

By:

Wang, Aoyi;
Peng, Haoyang;
Wang, Yingdong;
Zhang, Haoran;
Cheng, Caiping;
Zhao, Jinzhong;
Zhang, Wuxia;
Chen, Jianxin;
Li, Peng

Publication type:

Article

Revealing the antimicrobial potential of traditional Chinese medicine through text mining and molecular computation.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf077

By:

Chung, Meng-Chi;
Su, Li-Jen;
Chen, Chien-Lin;
Wu, Li-Ching

Publication type:

Article

scMitoMut for calling mitochondrial lineage-related mutations in single cells.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf072

By:

Sun, Wenjie;
Ginneken, Daphne van;
Perié, Leïla

Publication type:

Article

cfDiffusion: diffusion-based efficient generation of high quality scRNA-seq data with classifier-free guidance.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf071

By:

Zhang, Tianjiao;
Zhao, Zhongqian;
Ren, Jixiang;
Zhang, Ziheng;
Zhang, Hongfei;
Wang, Guohua

Publication type:

Article

A large language model framework for literature-based disease–gene association prediction.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf070

By:

Li, Peng-Hsuan;
Sun, Yih-Yun;
Juan, Hsueh-Fen;
Chen, Chien-Yu;
Tsai, Huai-Kuang;
Huang, Jia-Hsin

Publication type:

Article

DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf069

By:

Luo, Shijie;
Zhu, Ming;
Lin, Liquan;
Xie, Jiajing;
Lin, Shihao;
Chen, Ying;
Zhu, Jiali;
Huang, Jialiang

Publication type:

Article

Correction to: Unveiling cross-reactivity: implications for immune response modulation in cancer.

Published in:: 2025
Publication type:: Correction Notice

Noninvasive fetal genotyping using deep neural networks.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf067

By:

Schwammenthal, Yonathan;
Rabinowitz, Tom;
Basel-Salmon, Lina;
Tomashov-Matar, Reut;
Shomron, Noam

Publication type:

Article

ESM-BBB-Pred: a fine-tuned ESM 2.0 and deep neural networks for the identification of blood–brain barrier peptides.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf066

By:

Naseem, Ansar;
Alturise, Fahad;
Alkhalifah, Tamim;
Khan, Yaser Daanial

Publication type:

Article

Correction to: STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution.

Published in:: 2025
Publication type:: Correction Notice

CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf063

By:

Park, Sehi;
Chong, Kil To;
Tayara, Hilal

Publication type:

Article

CSGDN: contrastive signed graph diffusion network for predicting crop gene–phenotype associations.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf062

By:

Pan, Yiru;
Ji, Xingyu;
You, Jiaqi;
Li, Lu;
Liu, Zhenping;
Zhang, Xianlong;
Zhang, Zeyu;
Wang, Maojun

Publication type:

Article

FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf061

By:

Wei, Yanming;
Zhou, Tong;
Zhai, Yixiao;
Yu, Liang;
Zou, Quan

Publication type:

Article

Response to Letter to Editor by A. Derbalah et al.: the role of automation in enhancing reproducibility and interoperability of PBPK models.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf060

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

Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf059

By:

Shen, Xiaotao;
Chen, Songjie;
Liang, Liang;
Avina, Monika;
Zackriah, Hanyah;
Jelliffe-Pawlowski, Laura;
Rand, Larry;
Snyder, Michael P

Publication type:

Article

mmGEBLUP: an advanced genomic prediction scheme for genetic improvement of complex traits in crops through integrative analysis of major genes, polygenes, and genotype–environment interactions.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf058

By:

Zhang, Qi-Xin;
Zhu, Tianneng;
Lin, Feng;
Fang, Dunhuang;
Chen, Xuejun;
Lou, Xiangyang;
Tong, Zhijun;
Xiao, Bingguang;
Xu, Hai-Ming

Publication type:

Article

PTTM: dissecting the profile of tumor tissue microbiome to reveal microbiota features and associations with host transcriptome.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf057

By:

Yao, Ruiqian;
Sun, Lu;
Gao, Ruifang;
Mei, Yue;
Xue, Geng;
Yu, Dong

Publication type:

Article

Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf056

By:

Lu, Qiqi;
Liu, Zhixian;
Wang, Xiaosheng

Publication type:

Article

Advances of computational methods enhance the development of multi-epitope vaccines.

Published in:

2025

By:

Wei, Yiwen;
Qiu, Tianyi;
Ai, Yisi;
Zhang, Yuxi;
Xie, Junting;
Zhang, Dong;
Luo, Xiaochuan;
Sun, Xiulan;
Wang, Xin;
Qiu, Jingxuan

Publication type:

Literature Review

iDOMO: identification of drug combinations via multi-set operations for treating diseases.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf054

By:

Zhou, Xianxiao;
Wu, Ling;
Wang, Minghui;
Wu, Guojun;
Zhang, Bin

Publication type:

Article

The role of automation in enhancing reproducibility and interoperability of PBPK models.

Published in:

2025

By:

Derbalah, Abdallah;
Jamei, Masoud;
Gardner, Iain;
Sepp, Armin

Publication type:

Letter to the Editor

Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf052

By:

Mo, Yuanyuan;
Liu, Juan;
Zhang, Lihua

Publication type:

Article

Semisynthetic simulation for microbiome data analysis.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf051

By:

Sankaran, Kris;
Kodikara, Saritha;
Li, Jingyi Jessica;
Cao, Kim-Anh Lê

Publication type:

Article

TransBic: bucket trend-preserving biclustering for finding local and interpretable expression patterns.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf050

By:

Li, Jing;
Mei, Qinglin;
Yang, Chaoxia;
Zhu, Naibo;
Li, Guojun

Publication type:

Article

Assessment of the functionality and usability of open-source rare variant analysis pipelines.

Published in:

2025

By:

Riccio, Cristian;
Jansen, Max L;
Thalén, Felix;
Koliopanos, Georgios;
Link, Vivian;
Ziegler, Andreas

Publication type:

Literature Review

Polygenic prediction for underrepresented populations through transfer learning by utilizing genetic similarity shared with European populations.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf048

By:

Zhu, Yiyang;
Chen, Wenying;
Zhu, Kexuan;
Liu, Yuxin;
Huang, Shuiping;
Zeng, Ping

Publication type:

Article

Do protein language models learn phylogeny?

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf047

By:

Tule, Sanjana;
Foley, Gabriel;
Bodén, Mikael

Publication type:

Article

Introducing TEC-LncMir for prediction of lncRNA-miRNA interactions through deep learning of RNA sequences.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf046

By:

Yang, Tingpeng;
He, Yonghong;
Wang, Yu

Publication type:

Article

Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf045

By:

Cinquin, Olivier

Publication type:

Article

Deciphering optimal molecular determinants of non-hemolytic, cell-penetrating antimicrobial peptides through bioinformatics and Random Forest.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf049

By:

Kumar, Ashok;
Chadha, Sonia;
Sharma, Mradul;
Kumar, Mukesh

Publication type:

Article

Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf043

By:

Yang, Bo;
Cui, Chenxi;
Wang, Meng;
Ji, Hong;
Gao, Feiyue

Publication type:

Article

Benchmarking 13 tools for mutational signature attribution, including a new and improved algorithm.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf042

By:

Jiang, Nanhai;
Wu, Yang;
Rozen, Steven G

Publication type:

Article

ViTax: adaptive hierarchical viral taxonomy classification with a taxonomy belief tree on a foundation model.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf041

By:

He, YuShuang;
Zhou, Feng;
Bai, JiaXing;
Gao, YiChun;
Huang, Xiaobing;
Wang, Ying

Publication type:

Article

Challenges and opportunities of developing bioinformatics platforms in Africa: the case of BurkinaBioinfo at Joseph Ki-Zerbo University, Burkina Faso.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf040

By:

Tibiri, Ezechiel B;
Boua, Palwende R;
Soulama, Issiaka;
Dubreuil-Tranchant, Christine;
Tando, Ndomassi;
Tollenaere, Charlotte;
Brugidou, Christophe;
Nanema, Romaric K;
Tiendrebeogo, Fidèle

Publication type:

Article

Classification-based pathway analysis using GPNet with novel P-value computation.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf039

By:

Lu, Hao;
Rezapour, Mostafa;
Baha, Haseebullah;
Niazi, Muhammad Khalid Khan;
Narayanan, Aarthi;
Gurcan, Metin Nafi

Publication type:

Article

Attention-aware differential learning for predicting peptide-MHC class I binding and T cell receptor recognition.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf038

By:

Niu, Rui;
Wang, Jingwei;
Li, Yanli;
Zhou, Jiren;
Guo, Yang;
Shang, Xuequn

Publication type:

Article

Inferring the genetic relationships between unsupervised deep learning–derived imaging phenotypes and glioblastoma through multi-omics approaches.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf037

By:

Ye, Liguo;
Ye, Cheng;
Li, Pengtao;
Wang, Yu;
Ma, Wenbin

Publication type:

Article

eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug–diet interactions.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf036

By:

Xu, Xiangnan;
Senior, Alistair M;
Couteur, David G Le;
Cogger, Victoria C;
Raubenheimer, David;
James, David E;
Parker, Benjamin;
Simpson, Stephen J;
Muller, Samuel;
Yang, Jean Y H

Publication type:

Article

SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf035

By:

Potente, Sara;
Boscarino, Diego;
Paladin, Dino;
Marchini, Sergio;
Beltrame, Luca;
Romualdi, Chiara

Publication type:

Article

Correction to: BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation.

Published in:: 2025
Publication type:: Correction Notice

B-Lightning: using bait genes for marker gene hunting in single-cell data with complex heterogeneity.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf033

By:

Shao, Yiren;
Gao, Qi;
Wang, Liuyang;
Li, Dongmei;
Nixon, Andrew B;
Chan, Cliburn;
Li, Qi-Jing;
Xie, Jichun

Publication type:

Article

Novel genetic insight for psoriasis: integrative genome-wide analyses in 863 080 individuals and proteome-wide Mendelian randomization.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf032

By:

Liu, Shunying;
Li, Lingfei;
Liang, Yi;
Tan, Yang;
Wang, Xiaoyu;
Feng, Yanhai;
Chen, Nian;
Lei, Xia

Publication type:

Article

Cell-type deconvolution for bulk RNA-seq data using single-cell reference: a comparative analysis and recommendation guideline.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf031

By:

Xu, Xintian;
Li, Rui;
Mo, Ouyang;
Liu, Kai;
Li, Justin;
Hao, Pei

Publication type:

Article

A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf030

By:

Feng, Xikang;
Huo, Miaozhe;
Li, He;
Yang, Yongze;
Jiang, Yuepeng;
He, Liang;
Li, Shuai Cheng

Publication type:

Article

Incremental modelling and analysis of biological systems with fuzzy hybrid Petri nets.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf029

By:

Assaf, George;
Liu, Fei;
Heiner, Monika

Publication type:

Article

Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf028

By:

Zhang, Zheyang;
Tang, Ronghan;
Zhu, Ming;
Zhu, Zhijuan;
Zhu, Jiali;
Li, Hua;
Tong, Mengsha;
Li, Nainong;
Huang, Jialiang

Publication type:

Article

Post-transcriptional regulation supports the homeostatic expression of mature RNA.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf027

By:

Su, Zheng;
Fang, Mingyan;
Smolnikov, Andrei;
Vafaee, Fatemeh;
Dinger, Marcel E;
Oates, Emily C

Publication type:

Article

TargetCLP: clathrin proteins prediction combining transformed and evolutionary scale modeling-based multi-view features via weighted feature integration approach.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf026

By:

Ullah, Matee;
Akbar, Shahid;
Raza, Ali;
Khan, Kashif Ahmad;
Zou, Quan

Publication type:

Article

BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1093/bib/bbaf025

By:

Yang, Yang;
Zheng, Zixuan;
Xu, Yuyang;
Wei, Huifang;
Yan, Wenying

Publication type:

Article