Works matching IS 14675463 AND DT 2023 AND VI 24 AND IP 5

Results: 69

Defining the single base importance of human mRNAs and lncRNAs.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad321

By:

Fan, Rui;
Ji, Xiangwen;
Li, Jianwei;
Cui, Qinghua;
Cui, Chunmei

Publication type:

Article

Sequence Alignment/Map format: a comprehensive review of approaches and applications.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad320

By:

Liu, Yuansheng;
Shen, Xiangzhen;
Gong, Yongshun;
Liu, Yiping;
Song, Bosheng;
Zeng, Xiangxiang

Publication type:

Article

Letter to the editor: testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad322

By:

Leventhal, Emily L;
Daamen, Andrea R;
Lipsky, Peter E

Publication type:

Article

3D based generative PROTAC linker design with reinforcement learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad323

By:

Li, Baiqing;
Ran, Ting;
Chen, Hongming

Publication type:

Article

Sequence-based prediction model of protein crystallization propensity using machine learning and two-level feature selection.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad319

By:

Le, Nguyen Quoc Khanh;
Li, Wanru;
Cao, Yanshuang

Publication type:

Article

Inferring single-cell gene regulatory network by non-redundant mutual information.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad326

By:

Zeng, Yanping;
He, Yongxin;
Zheng, Ruiqing;
Li, Min

Publication type:

Article

InDEP: an interpretable machine learning approach to predict cancer driver genes from multi-omics data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad318

By:

Yang, Hai;
Liu, Yawen;
Yang, Yijing;
Li, Dongdong;
Wang, Zhe

Publication type:

Article

Sequence pre-training-based graph neural network for predicting lncRNA-miRNA associations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad317

By:

Wang, Zixiao;
Liang, Shiyang;
Liu, Siwei;
Meng, Zhaohan;
Wang, Jingjie;
Liang, Shangsong

Publication type:

Article

The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad302

By:

Raffo, Andrea;
Paulsen, Jonas

Publication type:

Article

SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad315

By:

Lee, Lindsay;
Yu, Miao;
Li, Xiaoqi;
Zhu, Chenxu;
Zhang, Yanxiao;
Yu, Hongyu;
Chen, Ziyin;
Mishra, Shreya;
Ren, Bing;
Li, Yun;
Hu, Ming

Publication type:

Article

Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer – bioinformatics study for a potential link to MMEJ.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad314

By:

Kim, Pora;
Kumar, Himansu;
Yang, Chengyuan;
Luo, Ruihan;
Liu, Jiajia;
Zhou, Xiaobo

Publication type:

Article

Multimodal deep learning approaches for single-cell multi-omics data integration.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad313

By:

Athaya, Tasbiraha;
Ripan, Rony Chowdhury;
Li, Xiaoman;
Hu, Haiyan

Publication type:

Article

MFPred: prediction of ncRNA families based on multi-feature fusion.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad303

By:

Chen, Kai;
Zhu, Xiaodong;
Wang, Jiahao;
Zhao, Ziqi;
Hao, Lei;
Guo, Xinsheng;
Liu, Yuanning

Publication type:

Article

DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad316

By:

Zhang, Tianjiao;
Li, Liangyu;
Sun, Hailong;
Xu, Dali;
Wang, Guohua

Publication type:

Article

ML-PLIC: a web platform for characterizing protein–ligand interactions and developing machine learning-based scoring functions.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad295

By:

Zhang, Xujun;
Shen, Chao;
Wang, Tianyue;
Deng, Yafeng;
Kang, Yu;
Li, Dan;
Hou, Tingjun;
Pan, Peichen

Publication type:

Article

Identifying potential small molecule–miRNA associations via Robust PCA based on γ-norm regularization.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad312

By:

Wang, Shudong;
Ren, Chuanru;
Zhang, Yulin;
Li, Yunyin;
Pang, Shanchen;
Song, Tao

Publication type:

Article

NCAE: data-driven representations using a deep network-coherent DNA methylation autoencoder identify robust disease and risk factor signatures.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad293

By:

Martínez-Enguita, David;
Dwivedi, Sanjiv K;
Jörnsten, Rebecka;
Gustafsson, Mika

Publication type:

Article

HiFun: homology independent protein function prediction by a novel protein-language self-attention model.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad311

By:

Wu, Jun;
Qing, Haipeng;
Ouyang, Jian;
Zhou, Jiajia;
Gao, Zihao;
Mason, Christopher E;
Liu, Zhichao;
Shi, Tieliu

Publication type:

Article

MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein–protein interactions.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad310

By:

Yue, Yang;
Li, Shu;
Wang, Lingling;
Liu, Huanxiang;
Tong, Henry H Y;
He, Shan

Publication type:

Article

Multi-omics regulatory network inference in the presence of missing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad309

By:

Henao, Juan D;
Lauber, Michael;
Azevedo, Manuel;
Grekova, Anastasiia;
Theis, Fabian;
List, Markus;
Ogris, Christoph;
Schubert, Benjamin

Publication type:

Article

Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad308

By:

Turzo, S M Bargeen Alam;
Seffernick, Justin T;
Lyskov, Sergey;
Lindert, Steffen

Publication type:

Article

TransFoxMol: predicting molecular property with focused attention.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad306

By:

Gao, Jian;
Shen, Zheyuan;
Xie, Yufeng;
Lu, Jialiang;
Lu, Yang;
Chen, Sikang;
Bian, Qingyu;
Guo, Yue;
Shen, Liteng;
Wu, Jian;
Zhou, Binbin;
Hou, Tingjun;
He, Qiaojun;
Che, Jinxin;
Dong, Xiaowu

Publication type:

Article

A systematic benchmark of machine learning methods for protein–RNA interaction prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad307

By:

Horlacher, Marc;
Cantini, Giulia;
Hesse, Julian;
Schinke, Patrick;
Goedert, Nicolas;
Londhe, Shubhankar;
Moyon, Lambert;
Marsico, Annalisa

Publication type:

Article

HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad305

By:

Han, Shen;
Fu, Haitao;
Wu, Yuyang;
Zhao, Ganglan;
Song, Zhenyu;
Huang, Feng;
Zhang, Zhongfei;
Liu, Shichao;
Zhang, Wen

Publication type:

Article

A denoised multi-omics integration framework for cancer subtype classification and survival prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad304

By:

Pang, Jiali;
Liang, Bilin;
Ding, Ruifeng;
Yan, Qiujuan;
Chen, Ruiyao;
Xu, Jie

Publication type:

Article

KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad292

By:

Wu, Jinyang;
Ning, Zhiwei;
Ding, Yidong;
Wang, Ying;
Peng, Qinke;
Fu, Laiyi

Publication type:

Article

PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. N.PAG, doi. 10.1093/bib/bbad291

By:

Li, Yan;
Zhang, Shao-Wu;
Xie, Ming-Yu;
Zhang, Tong

Publication type:

Article

PredLLPS_PSSM: a novel predictor for liquid–liquid protein separation identification based on evolutionary information and a deep neural network.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad299

By:

Zhou, Shengming;
Zhou, Yetong;
Liu, Tian;
Zheng, Jia;
Jia, Cangzhi

Publication type:

Article

OTTM: an automated classification tool for translational drug discovery from omics data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad301

By:

Yang, Xiaobo;
Zhang, Bei;
Wang, Siqi;
Lu, Ye;
Chen, Kaixian;
Luo, Cheng;
Sun, Aihua;
Zhang, Hao

Publication type:

Article

Differential variability analysis of single-cell gene expression data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad294

By:

Liu, Jiayi;
Kreimer, Anat;
Li, Wei Vivian

Publication type:

Article

A fast and globally optimal solution for RNA-seq quantification.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad298

By:

Yi, Huiguang;
Lin, Yanling;
Chang, Qing;
Jin, Wenfei

Publication type:

Article

Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad297

By:

Yi, Dohun;
Nam, Jin-Wu;
Jeong, Hyobin

Publication type:

Article

Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad296

By:

Xie, Ailin;
Zhang, Ziqiao;
Guan, Jihong;
Zhou, Shuigeng

Publication type:

Article

ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad290

By:

Wang, He;
Zang, Yongjian;
Kang, Ying;
Zhang, Jianwen;
Zhang, Lei;
Zhang, Shengli

Publication type:

Article

Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad289

By:

Qiu, Yuchi;
Wei, Guo-Wei

Publication type:

Article

TMKit: a Python interface for computational analysis of transmembrane proteins.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad288

By:

Sun, Jianfeng;
Kulandaisamy, Arulsamy;
Ru, Jinlong;
Gromiha, M Michael;
Cribbs, Adam P

Publication type:

Article

HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad286

By:

Liu, Yuhang;
Wang, Zixuan;
Yuan, Hao;
Zhu, Guiquan;
Zhang, Yongqing

Publication type:

Article

COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad280

By:

Lim, Hendrick Gao-Min;
Fann, Yang C;
Lee, Yuan-Chii Gladys

Publication type:

Article

Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad278

By:

Shi, Xuejing;
Zhu, Juntong;
Long, Yahui;
Liang, Cheng

Publication type:

Article

Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad284

By:

Wang, Robert;
Helbig, Ingo;
Edmondson, Andrew C;
Lin, Lan;
Xing, Yi

Publication type:

Article

A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug–drug interaction data and supervised contrastive learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad285

By:

Gu, Jeonghyeon;
Bang, Dongmin;
Yi, Jungseob;
Lee, Sangseon;
Kim, Dong Kyu;
Kim, Sun

Publication type:

Article

DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad277

By:

Wu, Guiying;
Song, Mengmeng;
Wang, Ke;
Cui, Tianyu;
Jiao, Zicong;
Ji, Liyan;
Gao, Xuan;
Wang, Jiayin;
Liu, Tao;
Xia, Xuefeng;
Fang, Huan;
Guan, Yanfang;
Yi, Xin

Publication type:

Article

HiBrowser: an interactive and dynamic browser for synchronous Hi-C data visualization.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad283

By:

Li, Pingjing;
Liu, Hong;
Sun, Jialiang;
Lu, Jianguo;
Liu, Jian

Publication type:

Article

Deep multi-view contrastive learning for cancer subtype identification.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad282

By:

Chen, Wenlan;
Wang, Hong;
Liang, Cheng

Publication type:

Article

Single-cell causal network inferred by cross-mapping entropy.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad281

By:

Li, Lin;
Xia, Rui;
Chen, Wei;
Zhao, Qi;
Tao, Peng;
Chen, Luonan

Publication type:

Article

Multi-task prediction-based graph contrastive learning for inferring the relationship among lncRNAs, miRNAs and diseases.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad276

By:

Sheng, Nan;
Wang, Yan;
Huang, Lan;
Gao, Ling;
Cao, Yangkun;
Xie, Xuping;
Fu, Yuan

Publication type:

Article

Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad275

By:

Lu, Na;
Qiao, Yi;
An, Pengfei;
Luo, Jiajian;
Bi, Changwei;
Li, Musheng;
Lu, Zuhong;
Tu, Jing

Publication type:

Article

A workflow to study mechanistic indicators for driver gene prediction with Moonlight.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad274

By:

Nourbakhsh, Mona;
Saksager, Astrid;
Tom, Nikola;
Chen, Xi Steven;
Colaprico, Antonio;
Olsen, Catharina;
Tiberti, Matteo;
Papaleo, Elena

Publication type:

Article

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad279

By:

Cho, Hunyong;
Qu, Yixiang;
Liu, Chuwen;
Tang, Boyang;
Lyu, Ruiqi;
Lin, Bridget M;
Roach, Jeffrey;
Azcarate-Peril, M Andrea;
Ribeiro, Apoena Aguiar;
Love, Michael I;
Divaris, Kimon;
Wu, Di

Publication type:

Article

Approximate estimation of cell-type resolution transcriptome in bulk tissue through matrix completion.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad273

By:

Wang, Weixu;
Zhou, Xiaolan;
Wang, Jing;
Yao, Jun;
Wen, Haimei;
Wang, Yi;
Sun, Mingwan;
Zhang, Chao;
Tao, Wei;
Zou, Jiahua;
Ni, Ting

Publication type:

Article