Works matching IS 14675463 AND DT 2022 AND VI 23 AND IP 2

Results: 115

Correction to: PHR-search: a search framework for protein remote homology detection based on the predicted protein hierarchical relationships.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac103

By:

Jin, Xiaopeng;
Luo, Xiaoling;
Liu, Bin

Publication type:

Article

Letter regarding article named 'Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy'.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac065

By:

Zheng, Haizhen

Publication type:

Article

CRESSP: a comprehensive pipeline for prediction of immunopathogenic SARS-CoV-2 epitopes using structural properties of proteins.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac056

By:

An, Hyunsu;
Eun, Minho;
Yi, Jawoon;
Park, Jihwan

Publication type:

Article

Assessment of human microbiota stability across longitudinal samples using iteratively growing-partitioned clustering.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac055

By:

Sánchez-Sánchez, Pedro;
Santonja, Francisco J;
Benítez-Páez, Alfonso

Publication type:

Article

BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac053

By:

Tsukiyama, Sho;
Hasan, Md Mehedi;
Deng, Hong-Wen;
Kurata, Hiroyuki

Publication type:

Article

CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac049

By:

Rapti, Melivoia;
Zouaghi, Yassine;
Meylan, Jenny;
Ranza, Emmanuelle;
Antonarakis, Stylianos E;
Santoni, Federico A

Publication type:

Article

DLRAPom: a hybrid pipeline of Optimized XGBoost-guided integrative multiomics analysis for identifying targetable disease-related lncRNA–miRNA–mRNA regulatory axes.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac046

By:

Shen, Chen;
Li, Huiyu;
Li, Miao;
Niu, Yu;
Liu, Jing;
Zhu, Li;
Gui, Hongsheng;
Han, Wei;
Wang, Huiying;
Zhang, Wenpei;
Wang, Xiaochen;
Luo, Xiao;
Sun, Yu;
Yan, Jiangwei;
Guan, Fanglin

Publication type:

Article

MiRLoc: predicting miRNA subcellular localization by incorporating miRNA–mRNA interactions and mRNA subcellular localization.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac044

By:

Xu, Mingmin;
Chen, Yuanyuan;
Xu, Zhihui;
Zhang, Liangyun;
Jiang, Hangjin;
Pian, Cong

Publication type:

Article

Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac043

By:

Balagué-Dobón, Laura;
Cáceres, Alejandro;
González, Juan R

Publication type:

Article

cropCSM: designing safe and potent herbicides with graph-based signatures.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac042

By:

Pires, Douglas E V;
Stubbs, Keith A;
Mylne, Joshua S;
Ascher, David B

Publication type:

Article

POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac040

By:

Li, Fengcheng;
Zhou, Ying;
Zhang, Ying;
Yin, Jiayi;
Qiu, Yunqing;
Gao, Jianqing;
Zhu, Feng

Publication type:

Article

PGS-server: accuracy, robustness and transferability of polygenic score methods for biobank scale studies.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac039

By:

Yang, Sheng;
Zhou, Xiang

Publication type:

Article

Simultaneous test and estimation of total genetic effect in eQTL integrative analysis through mixed models.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac038

By:

Wang, Ting;
Qiao, Jiahao;
Zhang, Shuo;
Wei, Yongyue;
Zeng, Ping

Publication type:

Article

Adapt-Kcr: a novel deep learning framework for accurate prediction of lysine crotonylation sites based on learning embedding features and attention architecture.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac037

By:

Li, Zutan;
Fang, Jingya;
Wang, Shining;
Zhang, Liangyun;
Chen, Yuanyuan;
Pian, Cong

Publication type:

Article

Shedding light on the hidden human proteome expands immunopeptidome in cancer.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac034

By:

Li, Yongsheng;
Zhang, Yunpeng;
Pan, Tao;
Zhou, Ping;
Zhou, Weiwei;
Gao, Yueying;
Zheng, Shaojiang;
Xu, Juan

Publication type:

Article

ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac033

By:

Zhang, Xiao-Chen;
Yi, Jia-Cai;
Yang, Guo-Ping;
Wu, Cheng-Kun;
Hou, Ting-Jun;
Cao, Dong-Sheng

Publication type:

Article

SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac030

By:

Yang, Tingting;
Gan, Mingyu;
Liu, Qingyun;
Liang, Wenying;
Tang, Qiqin;
Luo, Geyang;
Zuo, Tianyu;
Guo, Yongchao;
Hong, Chuangyue;
Li, Qibing;
Tan, Weiguo;
Gao, Qian

Publication type:

Article

ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac031

By:

Wang, Xiaoyu;
Li, Fuyi;
Xu, Jing;
Rong, Jia;
Webb, Geoffrey I;
Ge, Zongyuan;
Li, Jian;
Song, Jiangning

Publication type:

Article

Multi-variable AUC for sifting complementary features and its biomedical application.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac029

By:

Su, Yue;
Du, Keyu;
Wang, Jun;
Wei, Jin-mao;
Liu, Jian

Publication type:

Article

Librator: a platform for the optimized analysis, design, and expression of mutable influenza viral antigens.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac028

By:

Li, Lei;
Changrob, Siriruk;
Fu, Yanbin;
Stovicek, Olivia;
Guthmiller, Jenna J;
McGrath, Joshua J C;
Dugan, Haley L;
Stamper, Christopher T;
Zheng, Nai-Ying;
Huang, Min;
Wilson, Patrick C

Publication type:

Article

HCRNet: high-throughput circRNA-binding event identification from CLIP-seq data using deep temporal convolutional network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac027

By:

Yang, Yuning;
Hou, Zilong;
Wang, Yansong;
Ma, Hongli;
Sun, Pingping;
Ma, Zhiqiang;
Wong, Ka-Chun;
Li, Xiangtao

Publication type:

Article

Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac026

By:

Zhang, Biao;
Liu, Dong;
Zhang, Yang;
Shen, Hong-Bin;
Zhang, Gui-Jun

Publication type:

Article

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac025

By:

Pan, Qisheng;
Nguyen, Thanh Binh;
Ascher, David B;
Pires, Douglas E V

Publication type:

Article

Persistent spectral based ensemble learning (PerSpect-EL) for protein–protein binding affinity prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac024

By:

Wee, JunJie;
Xia, Kelin

Publication type:

Article

StackTADB: a stacking-based ensemble learning model for predicting the boundaries of topologically associating domains (TADs) accurately in fruit flies.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac023

By:

Wu, Hao;
Zhang, Pengyu;
Ai, Zhaoheng;
Wei, Leyi;
Zhang, Hongming;
Yang, Fan;
Cui, Lizhen

Publication type:

Article

Deep learning-based identification of genetic variants: application to Alzheimer's disease classification.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac022

By:

Jo, Taeho;
Nho, Kwangsik;
Bice, Paula;
Saykin, Andrew J;
Initiative, For The Alzheimer's Disease Neuroimaging

Publication type:

Article

Prediction of potential miRNA–disease associations based on stacked autoencoder.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac021

By:

Wang, Chun-Chun;
Li, Tian-Hao;
Huang, Li;
Chen, Xing

Publication type:

Article

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac020

By:

Marini, Simone;
Mora, Rodrigo A;
Boucher, Christina;
Noyes, Noelle Robertson;
Prosperi, Mattia

Publication type:

Article

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac019

By:

Yuan, Xiao;
Wang, Jing;
Dai, Bing;
Sun, Yanfang;
Zhang, Keke;
Chen, Fangfang;
Peng, Qian;
Huang, Yixuan;
Zhang, Xinlei;
Chen, Junru;
Xu, Xilin;
Chuan, Jun;
Mu, Wenbo;
Li, Huiyuan;
Fang, Ping;
Gong, Qiang;
Zhang, Peng

Publication type:

Article

Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac018

By:

Gan, Yanglan;
Huang, Xingyu;
Zou, Guobing;
Zhou, Shuigeng;
Guan, Jihong

Publication type:

Article

Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac017

By:

Anchang, Benedict;
Mendez-Giraldez, Raul;
Xu, Xiaojiang;
Archer, Trevor K;
Chen, Qing;
Hu, Guang;
Plevritis, Sylvia K;
Motsinger-Reif, Alison Anne;
Li, Jian-Liang

Publication type:

Article

Identifying drug–target interactions via heterogeneous graph attention networks combined with cross-modal similarities.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac016

By:

Jiang, Lu;
Sun, Jiahao;
Wang, Yue;
Ning, Qiao;
Luo, Na;
Yin, Minghao

Publication type:

Article

Predicting protein phosphorylation sites in soybean using interpretable deep tabular learning network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac015

By:

Khalili, Elham;
Ramazi, Shahin;
Ghanati, Faezeh;
Kouchaki, Samaneh

Publication type:

Article

SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac014

By:

Yang, Yaning;
Wang, Xiaoqi;
Zhou, Deshan;
Wei, Dong-Qing;
Peng, Shaoliang

Publication type:

Article

Computational analyses of bacterial strains from shotgun reads.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac013

By:

Ventolero, Minerva Fatimae;
Wang, Saidi;
Hu, Haiyan;
Li, Xiaoman

Publication type:

Article

IndGOterm: a qualitative method for the identification of individually dysregulated GO terms in cancer.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac012

By:

Zhang, Jiashuai;
Xiao, Huiting;
Song, Kai;
Li, Keru;
Yuan, Hengrui;
Yuan, Rongqiang;
Yang, Jia;
Zhao, Yuting;
Chang, Zhiqiang;
Zhao, Wenyuan

Publication type:

Article

RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac011

By:

Tang, Xubo;
Shang, Jiayu;
Sun, Yanni

Publication type:

Article

Assessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac010

By:

Rubio, Alejandro;
Jimenez, Juan;
Pérez-Pulido, Antonio J

Publication type:

Article

Learning multi-scale heterogenous network topologies and various pairwise attributes for drug–disease association prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac009

By:

Zhang, Hongda;
Cui, Hui;
Zhang, Tiangang;
Cao, Yangkun;
Xuan, Ping

Publication type:

Article

Accelerating the discovery of antifungal peptides using deep temporal convolutional networks.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac008

By:

Singh, Vishakha;
Shrivastava, Sameer;
Singh, Sanjay Kumar;
Kumar, Abhinav;
Saxena, Sonal

Publication type:

Article

review on the application of bioinformatics tools in food microbiome studies.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac007

By:

Chelliah, Ramachandran;
Banan-MwineDaliri, Eric;
Khan, Imran;
Wei, Shuai;
Elahi, Fazle;
Yeon, Su-Jung;
Selvakumar, Vijayalakshmi;
Ofosu, Fred Kwame;
Rubab, Momna;
Ju, Hum Hun;
Rallabandi, Harikrishna Reddy;
Madar, Inamul Hasan;
Sultan, Ghazala;
Oh, Deog Hwan

Publication type:

Article

Biomedical data, computational methods and tools for evaluating disease–disease associations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac006

By:

Xiang, Ju;
Zhang, Jiashuai;
Zhao, Yichao;
Wu, Fang-Xiang;
Li, Min

Publication type:

Article

Ontology-aware neural network: a general framework for pattern mining from microbiome data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac005

By:

Zha, Yuguo;
Ning, Kang

Publication type:

Article

Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac004

By:

Ruan, Zhi;
Zou, Shengmei;
Wang, Zeyu;
Zhang, Luhan;
Chen, Hangfei;
Wu, Yuye;
Jia, Huiqiong;
Draz, Mohamed S;
Feng, Ye

Publication type:

Article

Anc2vec: embedding gene ontology terms by preserving ancestors relationships.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac003

By:

Edera, Alejandro A;
Milone, Diego H;
Stegmayer, Georgina

Publication type:

Article

Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac002

By:

Wang, Ran;
Zheng, Xubin;
Wang, Jun;
Wan, Shibiao;
Song, Fangda;
Wong, Man Hon;
Leung, Kwong Sak;
Cheng, Lixin

Publication type:

Article

ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac001

By:

Shahid, Mahwish;
Ilyas, Maham;
Hussain, Waqar;
Khan, Yaser Daanial

Publication type:

Article

Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab610

By:

Yates, Josephine;
Boeva, Valentina

Publication type:

Article

PHR-search: a search framework for protein remote homology detection based on the predicted protein hierarchical relationships.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab609

By:

Jin, Xiaopeng;
Luo, Xiaoling;
Liu, Bin

Publication type:

Article

JEBIN: analyzing gene co-expressions across multiple datasets by joint network embedding.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab603

By:

Wu, Guiying;
Li, Xiangyu;
Guo, Wenbo;
Wei, Zheng;
Hu, Tao;
Shan, Yiran;
Gu, Jin

Publication type:

Article