Works matching IS 1471-2105 AND VI 22 AND DT 2021

Results: 632

Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors.

Published in:

2021

By:

Guan, Dengfeng;
McCarthy, Shane A.;
Ning, Zemin;
Wang, Guohua;
Wang, Yadong;
Durbin, Richard

Publication type:

Correction Notice

cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04529-2

By:

Qi, Meifang;
Nayar, Utthara;
Ludwig, Leif S.;
Wagle, Nikhil;
Rheinbay, Esther

Publication type:

Article

GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04461-5

By:

Marini, Federico;
Ludt, Annekathrin;
Linke, Jan;
Strauch, Konstantin

Publication type:

Article

Selected abstracts of Bioinformatics: from Algorithms to Applications 2021 Conference.

Published in:: BMC Bioinformatics, 2021, v. 22, n. 16, p. 1, doi. 10.1186/s12859-021-04475-z
Publication type:: Article

LDexpress: an online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04531-8

By:

Lin, Shu-Hong;
Thakur, Rohit;
Machiela, Mitchell J.

Publication type:

Article

pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04519-4

By:

Guerra, João Victor da Silva;
Ribeiro-Filho, Helder Veras;
Jara, Gabriel Ernesto;
Bortot, Leandro Oliveira;
Pereira, José Geraldo de Carvalho;
Lopes-de-Oliveira, Paulo Sérgio

Publication type:

Article

Class similarity network for coding and long non-coding RNA classification.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04517-6

By:

Zhang, Yu;
Long, Yahui;
Kwoh, Chee Keong

Publication type:

Article

FCLQC: fast and concurrent lossless quality scores compressor.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04516-7

By:

Cho, Minhyeok;
No, Albert

Publication type:

Article

COSNeti: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04510-z

By:

Martinez-Seidel, Federico;
Hsieh, Yin-Chen;
Walther, Dirk;
Kopka, Joachim;
Pereira Firmino, Alexandre Augusto

Publication type:

Article

Prioritising positively selected variants in whole-genome sequencing data using FineMAV.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04506-9

By:

Wahyudi, Fadilla;
Aghakhanian, Farhang;
Rahman, Sadequr;
Teo, Yik-Ying;
Szpak, Michał;
Dhaliwal, Jasbir;
Ayub, Qasim

Publication type:

Article

GraphOmics: an interactive platform to explore and integrate multi-omics data.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04500-1

By:

Wandy, Joe;
Daly, Rónán

Publication type:

Article

Gene prediction of aging-related diseases based on DNN and Mashup.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04518-5

By:

Ye, Junhua;
Wang, Shunfang;
Yang, Xin;
Tang, Xianjun

Publication type:

Article

Deep learning with language models improves named entity recognition for PharmaCoNER.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04260-y

By:

Sun, Cong;
Yang, Zhihao;
Wang, Lei;
Zhang, Yin;
Lin, Hongfei;
Wang, Jian

Publication type:

Article

Analyzing transfer learning impact in biomedical cross-lingual named entity recognition and normalization.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04247-9

By:

Rivera-Zavala, Renzo M.;
Martínez, Paloma

Publication type:

Article

Improving deep learning method for biomedical named entity recognition by using entity definition information.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04236-y

By:

Xiong, Ying;
Chen, Shuai;
Tang, Buzhou;
Chen, Qingcai;
Wang, Xiaolong;
Yan, Jun;
Zhou, Yi

Publication type:

Article

Combining word embeddings to extract chemical and drug entities in biomedical literature.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04188-3

By:

López-Úbeda, Pilar;
Díaz-Galiano, Manuel Carlos;
Ureña-López, L. Alfonso;
Martín-Valdivia, M. Teresa

Publication type:

Article

Concept recognition as a machine translation problem.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04141-4

By:

Boguslav, Mayla R.;
Hailu, Negacy D.;
Bada, Michael;
Baumgartner Jr., William A.;
Hunter, Lawrence E.

Publication type:

Article

GENPPI: standalone software for creating protein interaction networks from genomes.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04501-0

By:

Anjos, William F.;
Lanes, Gabriel C.;
Azevedo, Vasco A.;
Santos, Anderson R.

Publication type:

Article

qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE).

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04514-9

By:

Christie, Nanette;
Mannapperuma, Chanaka;
Ployet, Raphael;
van der Merwe, Karen;
Mähler, Niklas;
Delhomme, Nicolas;
Naidoo, Sanushka;
Mizrachi, Eshchar;
Street, Nathaniel R.;
Myburg, Alexander A.

Publication type:

Article

Primal-dual for classification with rejection (PD-CR): a novel method for classification and feature selection—an application in metabolomics studies.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04478-w

By:

Chardin, David;
Humbert, Olivier;
Bailleux, Caroline;
Burel-Vandenbos, Fanny;
Rigau, Valerie;
Pourcher, Thierry;
Barlaud, Michel

Publication type:

Article

Computational modelling of chromosomally clustering protein domains in bacteria.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04512-x

By:

Cotroneo, Chiara E.;
Gormley, Isobel Claire;
Shields, Denis C.;
Salter-Townshend, Michael

Publication type:

Article

gcMECM: graph clustering of mutual exclusivity of cancer mutations.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04505-w

By:

Hu, Ying;
Yan, Chunhua;
Chen, Qingrong;
Meerzaman, Daoud

Publication type:

Article

JLAN: medical code prediction via joint learning attention networks and denoising mechanism.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04520-x

By:

Li, Xingwang;
Zhang, Yijia;
Islam, Faiz ul;
Dong, Deshi;
Wei, Hao;
Lu, Mingyu

Publication type:

Article

AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04509-6

By:

Xiao, Li-Ming;
Wan, Yun-Qi;
Jiang, Zhen-Ran

Publication type:

Article

Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04513-w

By:

Sun, Ruya;
Zhou, Yuan;
Cui, Qinghua

Publication type:

Article

MCKAT: a multi-dimensional copy number variant kernel association test.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04494-w

By:

Maus Esfahani, Nastaran;
Catchpoole, Daniel;
Khan, Javed;
Kennedy, Paul J.

Publication type:

Article

Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04483-z

By:

Madjar, Katrin;
Zucknick, Manuela;
Ickstadt, Katja;
Rahnenführer, Jörg

Publication type:

Article

Correction to: Mining a stroke knowledge graph from literature.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04502-z

By:

Yang, Xi;
Wu, Chengkun;
Nenadic, Goran;
Wang, Wei;
Lu, Kai

Publication type:

Article

Optimal dimensionality selection for independent component analysis of transcriptomic data.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04497-7

By:

McConn, John Luke;
Lamoureux, Cameron R.;
Poudel, Saugat;
Palsson, Bernhard O.;
Sastry, Anand V.

Publication type:

Article

Five crucial prognostic-related autophagy genes stratified female breast cancer patients aged 40–60 years.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04503-y

By:

Li, Xiaolong;
Zhang, Hengchao;
Liu, Jingjing;
Li, Ping;
Sun, Yi

Publication type:

Article

Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet.

Published in:

2021

By:

Wang, Linyu;
Zhong, Xiaodan;
Wang, Shuo;
Liu, Yuanning

Publication type:

Correction Notice

An efficient scRNA-seq dropout imputation method using graph attention network.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04493-x

By:

Xu, Chenyang;
Cai, Lei;
Gao, Jingyang

Publication type:

Article

SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04492-y

By:

Liu, Zao;
Chen, Zhiwei;
Song, Kan

Publication type:

Article

ncDLRES: a novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04365-4

By:

Wang, Linyu;
Zhong, Xiaodan;
Wang, Shuo;
Liu, Yuanning

Publication type:

Article

QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04474-0

By:

Pereyra, Marc;
Drusko, Armin;
Krämer, Franziska;
Strobl, Frederic;
Stelzer, Ernst H. K.;
Matthäus, Franziska

Publication type:

Article

BreakNet: detecting deletions using long reads and a deep learning approach.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04499-5

By:

Luo, Junwei;
Ding, Hongyu;
Shen, Jiquan;
Zhai, Haixia;
Wu, Zhengjiang;
Yan, Chaokun;
Luo, Huimin

Publication type:

Article

Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04498-6

By:

Zhang, Junpeng;
Liu, Lin;
Xu, Taosheng;
Zhang, Wu;
Zhao, Chunwen;
Li, Sijing;
Li, Jiuyong;
Rao, Nini;
Le, Thuc Duy

Publication type:

Article

Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04491-z

By:

Mavaie, Pegah;
Holder, Lawrence;
Beck, Daniel;
Skinner, Michael K.

Publication type:

Article

Nested Stochastic Block Models applied to the analysis of single cell data.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04489-7

By:

Morelli, Leonardo;
Giansanti, Valentina;
Cittaro, Davide

Publication type:

Article

Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04488-8

By:

Sinha, Neeraj;
van Schothorst, Evert M.;
Hooiveld, Guido J. E. J.;
Keijer, Jaap;
Martins dos Santos, Vitor A. P.;
Suarez-Diez, Maria

Publication type:

Article

Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04488-8

By:

Sinha, Neeraj;
van Schothorst, Evert M.;
Hooiveld, Guido J. E. J.;
Keijer, Jaap;
Martins dos Santos, Vitor A. P.;
Suarez-Diez, Maria

Publication type:

Article

Bipartite graph-based collaborative matrix factorization method for predicting miRNA-disease associations.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04486-w

By:

Zhou, Feng;
Yin, Meng-Meng;
Jiao, Cui-Na;
Cui, Zhen;
Zhao, Jing-Xiu;
Liu, Jin-Xing

Publication type:

Article

A multitask transfer learning framework for the prediction of virus-human protein–protein interactions.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04484-y

By:

Dong, Thi Ngan;
Brogden, Graham;
Gerold, Gisa;
Khosla, Megha

Publication type:

Article

Predictive modeling of gene expression regulation.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04481-1

By:

Regondi, Chiara;
Fratelli, Maddalena;
Damia, Giovanna;
Guffanti, Federica;
Ganzinelli, Monica;
Matteucci, Matteo;
Masseroli, Marco

Publication type:

Article

EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04480-2

By:

MacDonald, Madolyn L.;
Lee, Kelvin H.

Publication type:

Article

Efficient iterative Hi-C scaffolder based on N-best neighbors.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04453-5

By:

Guan, Dengfeng;
McCarthy, Shane A.;
Ning, Zemin;
Wang, Guohua;
Wang, Yadong;
Durbin, Richard

Publication type:

Article

LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04485-x

By:

Zhou, Liqian;
Duan, Qi;
Tian, Xiongfei;
Xu, He;
Tang, Jianxin;
Peng, Lihong

Publication type:

Article

TSEBRA: transcript selector for BRAKER.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04482-0

By:

Gabriel, Lars;
Hoff, Katharina J.;
Brůna, Tomáš;
Borodovsky, Mark;
Stanke, Mario

Publication type:

Article

NeuRank: learning to rank with neural networks for drug–target interaction prediction.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04476-y

By:

Wu, Xiujin;
Zeng, Wenhua;
Lin, Fan;
Zhou, Xiuze

Publication type:

Article

TSEBRA: transcript selector for BRAKER.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04482-0

By:

Gabriel, Lars;
Hoff, Katharina J.;
Brůna, Tomáš;
Borodovsky, Mark;
Stanke, Mario

Publication type:

Article