Works matching IS 14675463 AND DT 2024 AND VI 25 AND IP 4

Results: 112

Comparative analyses of gene networks mediating cancer metastatic potentials across lineage types.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae357

By:

Wang, Sheng;
Stroup, Emily K;
Wang, Ting-You;
Yang, Rendong;
Ji, Zhe

Publication type:

Article

Unveiling promising drug targets for autism spectrum disorder: insights from genetics, transcriptomics, and proteomics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae353

By:

Jiang, Rui;
Huang, Wentao;
Qiu, Xinqi;
Chen, Jianyi;
Luo, Ruibang;
Zeng, Ruijie;
Tong, Shuangshuang;
Lyu, Yanlin;
Sun, Panpan;
Lian, Qizhou;
Leung, Felix W;
Liu, Yufeng;
Sha, Weihong;
Chen, Hao

Publication type:

Article

Precision probiotics supplement strategy in aging population based on gut microbiome composition.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae351

By:

Chuang, Yi-Fang;
Fan, Kang-Chen;
Su, Yin-Yuan;
Wu, Ming-Fong;
Chiu, Yen-Ling;
Liu, Yi-Chien;
Lin, Chen-Ching

Publication type:

Article

Introducing enzymatic cleavage features and transfer learning realizes accurate peptide half-life prediction across species and organs.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae350

By:

Tan, Xiaorong;
Liu, Qianhui;
Fang, Yanpeng;
Yang, Sen;
Chen, Fei;
Wang, Jianmin;
Ouyang, Defang;
Dong, Jie;
Zeng, Wenbin

Publication type:

Article

A large-scale assessment of sequence database search tools for homology-based protein function prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae349

By:

Zhang, Chengxin;
Freddolino, Lydia

Publication type:

Article

CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae348

By:

Fang, Yitian;
Luo, Mingshuang;
Ren, Zhixiang;
Wei, Leyi;
Wei, Dong-Qing

Publication type:

Article

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae347

By:

Farr, Elias;
Dimitrov, Daniel;
Schmidt, Christina;
Turei, Denes;
Lobentanzer, Sebastian;
Dugourd, Aurelien;
Saez-Rodriguez, Julio

Publication type:

Article

A survey of experimental and computational identification of small proteins.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae345

By:

Beals, Joshua;
Hu, Haiyan;
Li, Xiaoman

Publication type:

Article

Discovering predisposing genes for hereditary breast cancer using deep learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae346

By:

Passi, Gal;
Lieberman, Sari;
Zahdeh, Fouad;
Murik, Omer;
Renbaum, Paul;
Beeri, Rachel;
Linial, Michal;
May, Dalit;
Levy-Lahad, Ephrat;
Schneidman-Duhovny, Dina

Publication type:

Article

GEMF: a novel geometry-enhanced mid-fusion network for PLA prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae333

By:

Zhou, Guoqiang;
Qin, Yuke;
Hong, Qiansen;
Li, Haoran;
Chen, Huaming;
Shen, Jun

Publication type:

Article

Exploring functional conservation in silico: a new machine learning approach to RNA-editing.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae332

By:

Zawisza-Álvarez, Michał;
Peñuela-Melero, Jesús;
Vegas, Esteban;
Reverter, Ferran;
Garcia-Fernàndez, Jordi;
Herrera-Úbeda, Carlos

Publication type:

Article

Comparative analysis of integrative classification methods for multi-omics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae331

By:

Novoloaca, Alexei;
Broc, Camilo;
Beloeil, Laurent;
Yu, Wen-Han;
Becker, Jérémie

Publication type:

Article

EGPDI: identifying protein–DNA binding sites based on multi-view graph embedding fusion.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae330

By:

Zheng, Mengxin;
Sun, Guicong;
Li, Xueping;
Fan, Yongxian

Publication type:

Article

Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae329

By:

Wang, Tao;
Shu, Han;
Hu, Jialu;
Wang, Yongtian;
Chen, Jing;
Peng, Jiajie;
Shang, Xuequn

Publication type:

Article

A novel deep machine learning algorithm with dimensionality and size reduction approaches for feature elimination: thyroid cancer diagnoses with randomly missing data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae344

By:

Tutsoy, Onder;
Sumbul, Hilmi Erdem

Publication type:

Article

GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae343

By:

Jiang, Feng;
Guo, Yuzhi;
Ma, Hehuan;
Na, Saiyang;
Zhong, Wenliang;
Han, Yi;
Wang, Tao;
Huang, Junzhou

Publication type:

Article

Biclustering data analysis: a comprehensive survey.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae342

By:

Castanho, Eduardo N;
Aidos, Helena;
Madeira, Sara C

Publication type:

Article

Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae341

By:

Wang, Weibing;
Ye, Yusen;
Gao, Lin

Publication type:

Article

Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae340

By:

Xiang, Wenkai;
Zhong, Feisheng;
Ni, Lin;
Zheng, Mingyue;
Li, Xutong;
Shi, Qian;
Wang, Dingyan

Publication type:

Article

DeepIDA-GRU: a deep learning pipeline for integrative discriminant analysis of cross-sectional and longitudinal multiview data with applications to inflammatory bowel disease classification.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae339

By:

Jain, Sarthak;
Safo, Sandra E

Publication type:

Article

A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae338

By:

Tang, Xiangru;
Dai, Howard;
Knight, Elizabeth;
Wu, Fang;
Li, Yunyang;
Li, Tianxiao;
Gerstein, Mark

Publication type:

Article

MiRAGE: mining relationships for advanced generative evaluation in drug repositioning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae337

By:

Aragh, Aria Hassanali;
Givehchian, Pegah;
Amirani, Razieh Moslemi;
Masumshah, Raziyeh;
Eslahchi, Changiz

Publication type:

Article

SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae336

By:

Hu, Heng;
Gao, Runtian;
Gao, Wentao;
Gao, Bo;
Jiang, Zhongjun;
Zhou, Murong;
Wang, Guohua;
Jiang, Tao

Publication type:

Article

LDER-GE estimates phenotypic variance component of gene–environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae335

By:

Dong, Zihan;
Jiang, Wei;
Li, Hongyu;
DeWan, Andrew T;
Zhao, Hongyu

Publication type:

Article

DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae334

By:

Lei, Yahui;
Huang, Xiao-Tai;
Guo, Xingli;
Chan, Kei Hang Katie;
Gao, Lin

Publication type:

Article

RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae328

By:

Ianevski, Aleksandr;
Kushnir, Aleksandr;
Nader, Kristen;
Miihkinen, Mitro;
Xhaard, Henri;
Aittokallio, Tero;
Tanoli, Ziaurrehman

Publication type:

Article

Identifying pleiotropic genes via the composite test amidst the complexity of polygenic traits.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae327

By:

Lai, En-Yu;
Huang, Yen-Tsung

Publication type:

Article

CARTAR: a comprehensive web tool for identifying potential targets in chimeric antigen receptor therapies using TCGA and GTEx data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae326

By:

Hernandez-Gamarra, Miguel;
Salgado-Roo, Alba;
Dominguez, Eduardo;
Seco, Elena María Goiricelaya;
Veiga-Rúa, Sara;
Pedrera-Garbayo, Lucía F;
Carracedo, Ángel;
Allegue, Catarina

Publication type:

Article

ctGAN: combined transformation of gene expression and survival data with generative adversarial network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae325

By:

Kim, Jaeyoon;
Seok, Junhee

Publication type:

Article

PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae324

By:

Gupta, Sagar;
Kesarwani, Veerbhan;
Bhati, Umesh;
Jyoti;
Shankar, Ravi

Publication type:

Article

CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae323

By:

Kim, Yujin;
Jeong, Minwoo;
Koh, In Gyeong;
Kim, Chanhee;
Lee, Hyeji;
Kim, Jae Hyun;
Yurko, Ronald;
Kim, Il Bin;
Park, Jeongbin;
Werling, Donna M;
Sanders, Stephan J;
An, Joon-Yong

Publication type:

Article

PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae322

By:

Tian, Renmao;
Zhou, Jizhong;
Imanian, Behzad

Publication type:

Article

GLDADec: marker-gene guided LDA modeling for bulk gene expression deconvolution.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae315

By:

Azuma, Iori;
Mizuno, Tadahaya;
Kusuhara, Hiroyuki

Publication type:

Article

Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae314

By:

Chen, Hegang;
Lu, Yuyin;
Dai, Zhiming;
Yang, Yuedong;
Li, Qing;
Rao, Yanghui

Publication type:

Article

A cloud-based training module for efficient de novo transcriptome assembly using Nextflow and Google cloud.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae313

By:

Seaman, Ryan P;
Campbell, Ross;
Doe, Valena;
Yosufzai, Zelaikha;
Graber, Joel H

Publication type:

Article

Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae319

By:

Zhang, Guoqing;
Wang, Hui;
Zhang, Zhiguo;
Zhang, Lu;
Guo, Guibing;
Yang, Jian;
Yuan, Fajie;
Ju, Feng

Publication type:

Article

Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae320

By:

Gao, Yuan;
Ma, Bin;
Xu, Qianshuai;
Peng, Yuna;
Gong, Huimin;
Guan, Aohan;
Hua, Kexin;
Langford, Paul R;
Jin, Hui;
Luo, Rui

Publication type:

Article

DrugMetric: quantitative drug-likeness scoring based on chemical space distance.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae321

By:

Li, Bowen;
Wang, Zhen;
Liu, Ziqi;
Tao, Yanxin;
Sha, Chulin;
He, Min;
Li, Xiaolin

Publication type:

Article

Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae316

By:

Baul, Sudipto;
Ahmed, Khandakar Tanvir;
Jiang, Qibing;
Wang, Guangyu;
Li, Qian;
Yong, Jeongsik;
Zhang, Wei

Publication type:

Article

Characterizing efficient feature selection for single-cell expression analysis.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae317

By:

Cho, Juok;
Baik, Bukyung;
Nguyen, Hai C T;
Park, Daeui;
Nam, Dougu

Publication type:

Article

Design patterns for the construction of computational biological models.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae318

By:

Herajy, Mostafa;
Liu, Fei;
Heiner, Monika

Publication type:

Article

Phylogenetic inference of inter-population transmission rates for infectious diseases.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae312

By:

Gay, Skylar A;
Ellison, Gregory;
Xu, Jianing;
Yang, Jialin;
Wei, Yiliang;
Wu, Shaoyuan;
Yu, Lili;
Whalen, Christopher C;
Arnold, Jonathan;
Liu, Liang

Publication type:

Article

Detecting tipping points of complex diseases by network information entropy.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae311

By:

Lyu, Chengshang;
Chen, Lingxi;
Liu, Xiaoping

Publication type:

Article

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

Published in:: 2024
Publication type:: Correction Notice

Inference of gene regulatory networks based on directed graph convolutional networks.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae309

By:

Wei, Pi-Jing;
Guo, Ziqiang;
Gao, Zhen;
Ding, Zheng;
Cao, Rui-Fen;
Su, Yansen;
Zheng, Chun-Hou

Publication type:

Article

TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae308

By:

Chen, Nanjun;
Yu, Jixiang;
Zhe, Liu;
Wang, Fuzhou;
Li, Xiangtao;
Wong, Ka-Chun

Publication type:

Article

Antibody design using deep learning: from sequence and structure design to affinity maturation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae307

By:

Joubbi, Sara;
Micheli, Alessio;
Milazzo, Paolo;
Maccari, Giuseppe;
Ciano, Giorgio;
Cardamone, Dario;
Medini, Duccio

Publication type:

Article

Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae306

By:

Chen, Bijia;
Ren, Chao;
Ouyang, Zhangyi;
Xu, Jingxuan;
Xu, Kang;
Li, Yaru;
Guo, Hejiang;
Bai, Xuemei;
Tian, Mengge;
Xu, Xiang;
Wang, Yuyang;
Li, Hao;
Bo, Xiaochen;
Chen, Hebing

Publication type:

Article

scPLAN: a hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae305

By:

Guo, Qirui;
Yuan, Musu;
Zhang, Lei;
Deng, Minghua

Publication type:

Article

AttABseq: an attention-based deep learning prediction method for antigen–antibody binding affinity changes based on protein sequences.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae304

By:

Jin, Ruofan;
Ye, Qing;
Wang, Jike;
Cao, Zheng;
Jiang, Dejun;
Wang, Tianyue;
Kang, Yu;
Xu, Wanting;
Hsieh, Chang-Yu;
Hou, Tingjun

Publication type:

Article