Works in Briefings in Bioinformatics, 2024, Vol 25, Issue 5

Results: 104

Novel systems biology experimental pipeline reveals matairesinol's antimetastatic potential in prostate cancer: an integrated approach of network pharmacology, bioinformatics, and experimental validation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae466

By:

Rajadnya, Rama;
Sharma, Nidhi;
Mahajan, Akanksha;
Ulhe, Amrita;
Patil, Rajesh;
Hegde, Mahabaleshwar;
Mali, Aniket

Publication type:

Article

PELMI: Realize robust DNA image storage under general errors via parity encoding and local mean iteration.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae463

By:

Cao, Ben;
Wang, Kun;
Xie, Lei;
Zhang, Jianxia;
Zhao, Yunzhu;
Wang, Bin;
Zheng, Pan

Publication type:

Article

VISTA: an integrated framework for structural variant discovery.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae462

By:

Sarwal, Varuni;
Lee, Seungmo;
Yang, Jianzhi;
Sankararaman, Sriram;
Chaisson, Mark;
Eskin, Eleazar;
Mangul, Serghei

Publication type:

Article

ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae460

By:

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

Publication type:

Article

A high-dimensional omnibus test for set-based association analysis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae456

By:

Yang, Haitao;
Wang, Xin;
Zhang, Zechen;
Chen, Fuzhao;
Cao, Hongyan;
Yan, Lina;
Gao, Xia;
Dong, Hui;
Cui, Yuehua

Publication type:

Article

PGBind: pocket-guided explicit attention learning for protein–ligand docking.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae455

By:

Shen, Ao;
Yuan, Mingzhi;
Ma, Yingfan;
Du, Jie;
Wang, Manning

Publication type:

Article

NetMIM: network-based multi-omics integration with block missingness for biomarker selection and disease outcome prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae454

By:

Zhu, Bencong;
Zhang, Zhen;
Leung, Suet Yi;
Fan, Xiaodan

Publication type:

Article

Editorial.

Published in:

2024

By:

Ma, Shuangge

Publication type:

Editorial

GeneRaMeN enables integration, comparison, and meta-analysis of multiple ranked gene lists to identify consensus, unique, and correlated genes.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae452

By:

Yousefi, Meisam;
See, Wayne Ren;
Aw-Yong, Kam Leng;
Lee, Wai Suet;
Yong, Cythia Lingli;
Fanusi, Felic;
Smith, Gavin J D;
Ooi, Eng Eong;
Li, Shang;
Ghosh, Sujoy;
Ooi, Yaw Shin

Publication type:

Article

Analysis of sex-biased gene expression in a Eurasian admixed population.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae451

By:

Cheng, Shuangshuang;
Ning, Zhilin;
Huang, Ke;
Yuan, Yuan;
Tan, Xinjiang;
Pan, Yuwen;
Zhang, Rui;
Tian, Lei;
Lu, Yan;
Wang, Xiaoji;
Lu, Dongsheng;
Yang, Yajun;
Guan, Yaqun;
Mamatyusupu, Dolikun;
Xu, Shuhua

Publication type:

Article

Multi-omics integration for both single-cell and spatially resolved data based on dual-path graph attention auto-encoder.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae450

By:

Lv, Tongxuan;
Zhang, Yong;
Liu, Junlin;
Kang, Qiang;
Liu, Lin

Publication type:

Article

Designing interpretable deep learning applications for functional genomics: a quantitative analysis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae449

By:

Hilten, Arno van;
Katz, Sonja;
Saccenti, Edoardo;
Niessen, Wiro J;
Roshchupkin, Gennady V

Publication type:

Article

Multimodal functional deep learning for multiomics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae448

By:

Zhou, Yuan;
Geng, Pei;
Zhang, Shan;
Xiao, Feifei;
Cai, Guoshuai;
Chen, Li;
Initiative, For the Alzheimer's Disease Neuroimaging;
Lu, Qing

Publication type:

Article

Clinical bioinformatics desiderata for molecular tumor boards.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae447

By:

Pallocca, Matteo;
Betti, Martina;
Baldinelli, Sara;
Palombo, Ramona;
Bucci, Gabriele;
Mazzarella, Luca;
Tonon, Giovanni;
Ciliberto, Gennaro

Publication type:

Article

Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae446

By:

Wang, Xiaoyu;
Li, Fuyi;
Zhang, Yiwen;
Imoto, Seiya;
Shen, Hsin-Hui;
Li, Shanshan;
Guo, Yuming;
Yang, Jian;
Song, Jiangning

Publication type:

Article

AI-based IsAb2.0 for antibody design.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae445

By:

Liang, Tianjian;
Sun, Ze-Yu;
Hines, Margaret G;
Penrose, Kerri Jo;
Hao, Yixuan;
Chu, Xiaojie;
Mellors, John W;
Dimitrov, Dimiter S;
Xie, Xiang-Qun;
Li, Wei;
Feng, Zhiwei

Publication type:

Article

Reinforcement learning-driven exploration of peptide space: accelerating generation of drug-like peptides.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae444

By:

Wang, Qian;
Hu, Xiaotong;
Wei, Zhiqiang;
Lu, Hao;
Liu, Hao

Publication type:

Article

Global-local aware Heterogeneous Graph Contrastive Learning for multifaceted association prediction in miRNA–gene–disease networks.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae443

By:

Si, Yuxuan;
Huang, Zihan;
Fang, Zhengqing;
Yuan, Zhouhang;
Huang, Zhengxing;
Li, Yingming;
Wei, Ying;
Wu, Fei;
Yao, Yu-Feng

Publication type:

Article

Enhancing clinical genomic accuracy with panelGC: a novel metric and tool for quantifying and monitoring GC biases in hybridization capture panel sequencing.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae442

By:

Cheng, Xuanjin;
Goktas, Murathan T;
Williamson, Laura M;
Krzywinski, Martin;
Mulder, David T;
Swanson, Lucas;
Slind, Jill;
Sihvonen, Jelena;
Chow, Cynthia R;
Carr, Amy;
Bosdet, Ian;
Tucker, Tracy;
Young, Sean;
Moore, Richard;
Mungall, Karen L;
Yip, Stephen;
Jones, Steven J M

Publication type:

Article

Comprehensive assessment of long-read sequencing platforms and calling algorithms for detection of copy number variation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae441

By:

Yuan, Na;
Jia, Peilin

Publication type:

Article

Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae440

By:

Liu, Xin;
Pang, Yu;
Shan, Junqi;
Wang, Yunfei;
Zheng, Yanhua;
Xue, Yuhang;
Zhou, Xuerong;
Wang, Wenjun;
Sun, Yanlai;
Yan, Xiaojing;
Shi, Jiantao;
Wang, Xiaoxue;
Gu, Hongcang;
Zhang, Fan

Publication type:

Article

DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae439

By:

Zhao, Jian;
Chen, Zhewei;
Zhang, Meng;
Zou, Lingxiao;
He, Shan;
Liu, Jingjing;
Wang, Quan;
Song, Xiaofeng;
Wu, Jing

Publication type:

Article

Adapting differential molecular representation with hierarchical prompts for multi-label property prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae438

By:

Kang, Linjia;
Zhou, Songhua;
Fang, Shuyan;
Liu, Shichao

Publication type:

Article

ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae437

By:

Zhang, Min;
Zhang, Wensheng;
Ma, Xiaoke

Publication type:

Article

scHyper: reconstructing cell–cell communication through hypergraph neural networks.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae436

By:

Li, Wenying;
Wang, Haiyun;
Zhao, Jianping;
Xia, Junfeng;
Sun, Xiaoqiang

Publication type:

Article

ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae435

By:

Fan, Kechen;
Li, Mengfan;
Zhang, Jiarong;
Xie, Zihan;
Jiang, Daguang;
Bo, Xiaochen;
Zhao, Dongsheng;
Shi, Shenghui;
Ni, Ming

Publication type:

Article

Variable calling of m<sup>6</sup>A and associated features in databases: a guide for end-users.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae434

By:

Song, Renhua;
Sutton, Gavin J;
Li, Fuyi;
Liu, Qian;
Wong, Justin J-L

Publication type:

Article

A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae433

By:

Zhan, Lingmin;
Wang, Yingdong;
Wang, Aoyi;
Zhang, Yuanyuan;
Cheng, Caiping;
Zhao, Jinzhong;
Zhang, Wuxia;
Chen, Jianxin;
Li, Peng

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae432

By:

Zhao, Jiaying;
Ching, Wai-Ki;
Wong, Chi-Wing;
Cheng, Xiaoqing

Publication type:

Article

Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae431

By:

Xu, Zichang;
Ismanto, Hendra S;
Saputri, Dianita S;
Haruna, Soichiro;
Sun, Guanqun;
Wilamowski, Jan;
Teraguchi, Shunsuke;
Sengupta, Ayan;
Li, Songling;
Standley, Daron M

Publication type:

Article

Large language model produces high accurate diagnosis of cancer from end-motif profiles of cell-free DNA.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae430

By:

Liu, Jilei;
Shen, Hongru;
Chen, Kexin;
Li, Xiangchun

Publication type:

Article

Identification of molecular subtypes of dementia by using blood-proteins interaction-aware graph propagational network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae428

By:

Park, Sunghong;
Hong, Chang Hyung;
Son, Sang Joon;
Roh, Hyun Woong;
Kim, Doyoon;
Shin, Hyunjung;
Woo, Hyun Goo

Publication type:

Article

Correction to: Revolutionizing GPCR–ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery.

Published in:: 2024
Publication type:: Correction Notice

SnapHiC-G: identifying long-range enhancer–promoter interactions from single-cell Hi-C data via a global background model.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae426

By:

Liu, Weifang;
Zhong, Wujuan;
Giusti-Rodríguez, Paola;
Jiang, Zhiyun;
Wang, Geoffery W;
Sun, Huaigu;
Hu, Ming;
Li, Yun

Publication type:

Article

Synthetic lethal connectivity and graph transformer improve synthetic lethality prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae425

By:

Fan, Kunjie;
Gökbağ, Birkan;
Tang, Shan;
Li, Shangjia;
Huang, Yirui;
Wang, Lingling;
Cheng, Lijun;
Li, Lang

Publication type:

Article

CAIM: coverage-based analysis for identification of microbiome.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae424

By:

Acheampong, Daniel A;
Jenjaroenpun, Piroon;
Wongsurawat, Thidathip;
Kurilung, Alongkorn;
Pomyen, Yotsawat;
Kandel, Sangam;
Kunadirek, Pattapon;
Chuaypen, Natthaya;
Kusonmano, Kanthida;
Nookaew, Intawat

Publication type:

Article

Detecting microsatellite instability by length comparison of microsatellites in the 3′ untranslated region with RNA-seq.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae423

By:

Choi, Jin-Wook;
Lee, Jin-Ok;
Lee, Sejoon

Publication type:

Article

ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae422

By:

Li, Minghan;
Su, Yuqing;
Gao, Yanbo;
Tian, Weidong

Publication type:

Article

Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae421

By:

Mi, Haoyang;
Sivagnanam, Shamilene;
Ho, Won Jin;
Zhang, Shuming;
Bergman, Daniel;
Deshpande, Atul;
Baras, Alexander S;
Jaffee, Elizabeth M;
Coussens, Lisa M;
Fertig, Elana J;
Popel, Aleksander S

Publication type:

Article

BertTCR: a Bert-based deep learning framework for predicting cancer-related immune status based on T cell receptor repertoire.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae420

By:

Zhang, Min;
Cheng, Qi;
Wei, Zhenyu;
Xu, Jiayu;
Wu, Shiwei;
Xu, Nan;
Zhao, Chengkui;
Yu, Lei;
Feng, Weixing

Publication type:

Article

Enteropathway: the metabolic pathway database for the human gut microbiota.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae419

By:

Shiroma, Hirotsugu;
Darzi, Youssef;
Terajima, Etsuko;
Nakagawa, Zenichi;
Tsuchikura, Hirotaka;
Tsukuda, Naoki;
Moriya, Yuki;
Okuda, Shujiro;
Goto, Susumu;
Yamada, Takuji

Publication type:

Article

Multiview representation learning for identification of novel cancer genes and their causative biological mechanisms.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae418

By:

Yang, Jianye;
Fu, Haitao;
Xue, Feiyang;
Li, Menglu;
Wu, Yuyang;
Yu, Zhanhui;
Luo, Haohui;
Gong, Jing;
Niu, Xiaohui;
Zhang, Wen

Publication type:

Article

CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae417

By:

Li, Jianan;
Yanagisawa, Keisuke;
Akiyama, Yutaka

Publication type:

Article

Efficient test for deviation from Hardy–Weinberg equilibrium with known or ambiguous typing in highly polymorphic loci.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae416

By:

Shkuri, Or;
Israeli, Sapir;
Tshuva, Yuli;
Maiers, Martin;
Louzoun, Yoram

Publication type:

Article

Conjoint analysis of succinylome and phosphorylome reveals imbalanced HDAC phosphorylation-driven succinylayion dynamic contibutes to lung cancer.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae415

By:

Guo, Yifan;
Wen, Haoyu;
Chen, Zongwei;
Jiao, Mengxia;
Zhang, Yuchen;
Ge, Di;
Liu, Ronghua;
Gu, Jie

Publication type:

Article

HTINet2: herb–target prediction via knowledge graph embedding and residual-like graph neural network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae414

By:

Duan, Pengbo;
Yang, Kuo;
Su, Xin;
Fan, Shuyue;
Dong, Xin;
Zhang, Fenghui;
Li, Xianan;
Xing, Xiaoyan;
Zhu, Qiang;
Yu, Jian;
Zhou, Xuezhong

Publication type:

Article

DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae413

By:

Bai, Xin;
Yao, Hui-Cong;
Wu, Bo;
Liu, Luo-Ran;
Ding, Yu-Ying;
Xiao, Chuan-Le

Publication type:

Article

HHOMR: a hybrid high-order moment residual model for miRNA-disease association prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae412

By:

Li, Zhengwei;
Wan, Lipeng;
Wang, Lei;
Wang, Wenjing;
Nie, Ru

Publication type:

Article

CHAI: consensus clustering through similarity matrix integration for cell-type identification.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae411

By:

Lodi, Musaddiq K;
Lodi, Muzammil;
Osei, Kezie;
Ranganathan, Vaishnavi;
Hwang, Priscilla;
Ghosh, Preetam

Publication type:

Article

TME-NET: an interpretable deep neural network for predicting pan-cancer immune checkpoint inhibitor responses.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae410

By:

Ding, Xiaobao;
Zhang, Lin;
Fan, Ming;
Li, Lihua

Publication type:

Article