Works matching IS 14675463 AND DT 2021 AND VI 22 AND IP 1

Results: 55

Deep learning for drug response prediction in cancer.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 360, doi. 10.1093/bib/bbz171

By:

Baptista, Delora;
Ferreira, Pedro G;
Rocha, Miguel

Publication type:

Article

Design powerful predictor for mRNA subcellular location prediction in Homo sapiens.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 526, doi. 10.1093/bib/bbz177

By:

Zhang, Zhao-Yue;
Yang, Yu-He;
Ding, Hui;
Wang, Dong;
Chen, Wei;
Lin, Hao

Publication type:

Article

Closing the circle: current state and perspectives of circular RNA databases.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 288, doi. 10.1093/bib/bbz175

By:

Vromman, Marieke;
Vandesompele, Jo;
Volders, Pieter-Jan

Publication type:

Article

Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 497, doi. 10.1093/bib/bbz173

By:

Shen, Chao;
Hu, Ye;
Wang, Zhe;
Zhang, Xujun;
Zhong, Haiyang;
Wang, Gaoang;
Yao, Xiaojun;
Xu, Lei;
Cao, Dongsheng;
Hou, Tingjun

Publication type:

Article

Erratum to: Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 604, doi. 10.1093/bib/bbz172

By:

Galano-Frutos, Juan J;
García-Cebollada, Helena;
Sancho, Javier

Publication type:

Article

Computational annotation of miRNA transcription start sites.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 380, doi. 10.1093/bib/bbz178

By:

Wang, Saidi;
Talukder, Amlan;
Cha, Mingyu;
Li, Xiaoman;
Hu, Haiyan

Publication type:

Article

Deep learning-based clustering approaches for bioinformatics.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 393, doi. 10.1093/bib/bbz170

By:

Karim, Md Rezaul;
Beyan, Oya;
Zappa, Achille;
Costa, Ivan G;
Rebholz-Schuhmann, Dietrich;
Cochez, Michael;
Decker, Stefan

Publication type:

Article

EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 298, doi. 10.1093/bib/bbz169

By:

Lin, Shaofeng;
Wang, Chenwei;
Zhou, Jiaqi;
Shi, Ying;
Ruan, Chen;
Tu, Yiran;
Yao, Lan;
Peng, Di;
Xue, Yu

Publication type:

Article

On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 601, doi. 10.1093/bib/bbz168

By:

Savojardo, Castrense;
Martelli, Pier Luigi;
Casadio, Rita;
Fariselli, Piero

Publication type:

Article

SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 416, doi. 10.1093/bib/bbz166

By:

Dong, Meichen;
Thennavan, Aatish;
Urrutia, Eugene;
Li, Yun;
Perou, Charles M;
Zou, Fei;
Jiang, Yuchao

Publication type:

Article

Predicting drug-induced hepatotoxicity based on biological feature maps and diverse classification strategies.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 428, doi. 10.1093/bib/bbz165

By:

Su, Ran;
Wu, Huichen;
Liu, Xinyi;
Wei, Leyi

Publication type:

Article

A survey and systematic assessment of computational methods for drug response prediction.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 232, doi. 10.1093/bib/bbz164

By:

Chen, Jinyu;
Zhang, Louxin

Publication type:

Article

Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 270, doi. 10.1093/bib/bbz161

By:

Kumar, Ammu Prasanna;
Verma, Chandra S;
Lukman, Suryani

Publication type:

Article

Human body-fluid proteome: quantitative profiling and computational prediction.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 315, doi. 10.1093/bib/bbz160

By:

Huang, Lan;
Shao, Dan;
Wang, Yan;
Cui, Xueteng;
Li, Yufei;
Chen, Qian;
Cui, Juan

Publication type:

Article

NCMCMDA: miRNA–disease association prediction through neighborhood constraint matrix completion.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 485, doi. 10.1093/bib/bbz159

By:

Chen, Xing;
Sun, Lian-Gang;
Zhao, Yan

Publication type:

Article

Toward a gold standard for benchmarking gene set enrichment analysis.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 545, doi. 10.1093/bib/bbz158

By:

Geistlinger, Ludwig;
Csaba, Gergely;
Santarelli, Mara;
Ramos, Marcel;
Schiffer, Lucas;
Turaga, Nitesh;
Law, Charity;
Davis, Sean;
Carey, Vincent;
Morgan, Martin;
Zimmer, Ralf;
Waldron, Levi

Publication type:

Article

Machine learning approaches and databases for prediction of drug–target interaction: a survey paper.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 247, doi. 10.1093/bib/bbz157

By:

Bagherian, Maryam;
Sabeti, Elyas;
Wang, Kai;
Sartor, Maureen A;
Nikolovska-Coleska, Zaneta;
Najarian, Kayvan

Publication type:

Article

Deep learning for mining protein data.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 194, doi. 10.1093/bib/bbz156

By:

Shi, Qiang;
Chen, Weiya;
Huang, Siqi;
Wang, Yan;
Xue, Zhidong

Publication type:

Article

Current challenges and best-practice protocols for microbiome analysis.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 178, doi. 10.1093/bib/bbz155

By:

Bharti, Richa;
Grimm, Dominik G

Publication type:

Article

A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 581, doi. 10.1093/bib/bbz154

By:

Liu, Xueyan;
Xu, Yong;
Wang, Ran;
Liu, Sheng;
Wang, Jun;
Luo, YongLun;
Leung, Kwong-Sak;
Cheng, Lixin

Publication type:

Article

Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 346, doi. 10.1093/bib/bbz153

By:

Paltun, Betül Güvenç;
Mamitsuka, Hiroshi;
Kaski, Samuel

Publication type:

Article

DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 451, doi. 10.1093/bib/bbz152

By:

Chu, Yanyi;
Kaushik, Aman Chandra;
Wang, Xiangeng;
Wang, Wei;
Zhang, Yufang;
Shan, Xiaoqi;
Salahub, Dennis Russell;
Xiong, Yi;
Wei, Dong-Qing

Publication type:

Article

Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 463, doi. 10.1093/bib/bbz151

By:

Liu, Qi;
Ding, Changjun;
Lang, Xiaoqiang;
Guo, Ganggang;
Chen, Jiafei;
Su, Xiaohua

Publication type:

Article

BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 474, doi. 10.1093/bib/bbz150

By:

Dong, Jie;
Zhu, Min-Feng;
Yun, Yong-Huan;
Lu, Ai-Ping;
Hou, Ting-Jun;
Cao, Dong-Sheng

Publication type:

Article

Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 219, doi. 10.1093/bib/bbz149

By:

Magalhães, Beatriz T;
Lourenço, Anália;
Azevedo, Nuno F

Publication type:

Article

Drug–target prediction utilizing heterogeneous bio-linked network embeddings.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 568, doi. 10.1093/bib/bbz147

By:

Zong, Nansu;
Wong, Rachael Sze Nga;
Yu, Yue;
Wen, Andrew;
Huang, Ming;
Li, Ning

Publication type:

Article

Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 3, doi. 10.1093/bib/bbz146

By:

Galano-Frutos, Juan J;
García-Cebollada, Helena;
Sancho, Javier

Publication type:

Article

Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 308, doi. 10.1093/bib/bbz145

By:

O'Brien, Aidan R;
Burgio, Gaetan;
Bauer, Denis C

Publication type:

Article

A survey on adverse drug reaction studies: data, tasks and machine learning methods.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 164, doi. 10.1093/bib/bbz140

By:

Nguyen, Duc Anh;
Nguyen, Canh Hao;
Mamitsuka, Hiroshi

Publication type:

Article

The effect of tissue composition on gene co-expression.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 127, doi. 10.1093/bib/bbz135

By:

Zhang, Yun;
Cuerdo, Jonavelle;
Halushka, Marc K;
McCall, Matthew N

Publication type:

Article

CpG-island-based annotation and analysis of human housekeeping genes.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 515, doi. 10.1093/bib/bbz134

By:

Zhang, Le;
Dai, Zichun;
Yu, Jun;
Xiao, Ming

Publication type:

Article

An extensive review of tools for manual annotation of documents.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 146, doi. 10.1093/bib/bbz130

By:

Neves, Mariana;
Ševa, Jurica

Publication type:

Article

Current RNA-seq methodology reporting limits reproducibility.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 140, doi. 10.1093/bib/bbz124

By:

Simoneau, Joël;
Dumontier, Simon;
Gosselin, Ryan;
Scott, Michelle S

Publication type:

Article

Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 96, doi. 10.1093/bib/bbaa101

By:

Knyazev, Sergey;
Hughes, Lauren;
Skums, Pavel;
Zelikovsky, Alexander

Publication type:

Article

Hybrid modelling of biological systems using fuzzy continuous Petri nets.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 438, doi. 10.1093/bib/bbz114

By:

Liu, Fei;
Sun, Wujie;
Heiner, Monika;
Gilbert, David

Publication type:

Article

Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era—Editorial.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1093/bib/bbaa398

By:

Rombo, Simona E;
Ursino, Domenico

Publication type:

Article

Structured sparsity regularization for analyzing high-dimensional omics data.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 77, doi. 10.1093/bib/bbaa122

By:

Vinga, Susana

Publication type:

Article

The road towards data integration in human genomics: players, steps and interactions.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 30, doi. 10.1093/bib/bbaa080

By:

Bernasconi, Anna;
Canakoglu, Arif;
Masseroli, Marco;
Ceri, Stefano

Publication type:

Article

Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 610, doi. 10.1093/bib/bbaa106

By:

Schneider, Maria Victoria;
Jimenez, Rafael C

Publication type:

Article

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 109, doi. 10.1093/bib/bbz104

By:

Karp, Peter D;
Midford, Peter E;
Billington, Richard;
Kothari, Anamika;
Krummenacker, Markus;
Latendresse, Mario;
Ong, Wai Kit;
Subhraveti, Pallavi;
Caspi, Ron;
Fulcher, Carol;
Keseler, Ingrid M;
Paley, Suzanne M

Publication type:

Article

Using conceptual modeling to improve genome data management.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 45, doi. 10.1093/bib/bbaa100

By:

Pastor, Óscar;
León, Ana Palacio;
Reyes, José Fabián Román;
García, Alberto Simón;
Casamayor, Juan Carlos Rodenas

Publication type:

Article

Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 611, doi. 10.1093/bib/bbaa085

By:

Wang, Ziye;
Wang, Ying;
Fuhrman, Jed A;
Sun, Fengzhu;
Zhu, Shanfeng

Publication type:

Article

Comparison of microbiome samples: methods and computational challenges.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 88, doi. 10.1093/bib/bbaa121

By:

Comin, Matteo;
Camillo, Barbara Di;
Pizzi, Cinzia;
Vandin, Fabio

Publication type:

Article

Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 607, doi. 10.1093/bib/bbaa078

By:

Oh, Minsik;
Park, Sungjoon;
Kim, Sun;
Chae, Heejoon

Publication type:

Article

Computational methods for the integrative analysis of single-cell data.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 20, doi. 10.1093/bib/bbaa042

By:

Forcato, Mattia;
Romano, Oriana;
Bicciato, Silvio

Publication type:

Article

GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 55, doi. 10.1093/bib/bbaa033

By:

Gutiérrez-Sacristán, Alba;
Niz, Carlos De;
Kothari, Cartik;
Kong, Sek Won;
Mandl, Kenneth D;
Avillach, Paul

Publication type:

Article

Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 66, doi. 10.1093/bib/bbaa032

By:

Oh, Minsik;
Park, Sungjoon;
Kim, Sun;
Chae, Heejoon

Publication type:

Article

Closing the gap between formats for storing layout information in systems biology.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 608, doi. 10.1093/bib/bbaa030

By:

Hoksza, David;
Gawron, Piotr;
Ostaszewski, Marek;
Hasenauer, Jan;
Schneider, Reinhard

Publication type:

Article

Corrigendum to: Computational annotation of miRNA transcription start sites.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 609, doi. 10.1093/bib/bbaa024

By:

Wang, Saidi;
Talukder, Amlan;
Cha, Mingyu;
Li, Xiaoman;
Hu, Haiyan

Publication type:

Article

Erratum to: Machine learning approaches and databases for prediction of drug–target interaction: a survey paper.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 606, doi. 10.1093/bib/bbaa020

By:

Bagherian, Maryam;
Sabeti, Elyas;
Wang, Kai;
Sartor, Maureen A;
Nikolovska-Coleska, Zaneta;
Najarian, Kayvan

Publication type:

Article