Works matching IS 14675463 AND DT 2019

Results: 189

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2150, doi. 10.1093/bib/bby077

By:

Li, Fuyi;
Wang, Yanan;
Li, Chen;
Marquez-Lago, Tatiana T;
Leier, André;
Rawlings, Neil D;
Haffari, Gholamreza;
Revote, Jerico;
Akutsu, Tatsuya;
Chou, Kuo-Chen;
Purcell, Anthony W;
Pike, Robert N;
Webb, Geoffrey I;
Smith, A Ian;
Lithgow, Trevor;
Daly, Roger J;
Whisstock, James C;
Song, Jiangning

Publication type:

Article

TRCirc: a resource for transcriptional regulation information of circRNAs.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2327, doi. 10.1093/bib/bby083

By:

Tang, Zhidong;
Li, Xuecang;
Zhao, Jianmei;
Qian, Fengcui;
Feng, Chenchen;
Li, Yanyu;
Zhang, Jian;
Jiang, Yong;
Yang, Yongsan;
Wang, Qiuyu;
Li, Chunquan

Publication type:

Article

Sequencing era methods for identifying signatures of selection in the genome.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 1997, doi. 10.1093/bib/bby064

By:

Horscroft, Clare;
Ennis, Sarah;
Pengelly, Reuben J;
Sluckin, Timothy J;
Collins, Andrew

Publication type:

Article

A review of metrics measuring dissimilarity for rooted phylogenetic networks.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 1972, doi. 10.1093/bib/bby062

By:

Wang, Juan;
Guo, Maozu

Publication type:

Article

Review and comparative assessment of similarity-based methods for prediction of drug–protein interactions in the druggable human proteome.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2066, doi. 10.1093/bib/bby069

By:

Wang, Chen;
Kurgan, Lukasz

Publication type:

Article

Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2306, doi. 10.1093/bib/bby084

By:

Zou, Meng;
Jin, Rui;
Au, Kin Fai

Publication type:

Article

Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2028, doi. 10.1093/bib/bby066

By:

Nguyen, Dai Hai;
Nguyen, Canh Hao;
Mamitsuka, Hiroshi

Publication type:

Article

Quick approximation of threshold values for genome-wide association studies.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2217, doi. 10.1093/bib/bby082

By:

Hao, Zhiyu;
Jiang, Li;
Gao, Jin;
Ye, Jinhua;
Zhao, Jingli;
Li, Shuling;
Yang, Runqing

Publication type:

Article

Protein–peptide docking using CABS-dock and contact information.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2299, doi. 10.1093/bib/bby080

By:

Blaszczyk, Maciej;
Ciemny, Maciej Pawel;
Kolinski, Andrzej;
Kurcinski, Mateusz;
Kmiecik, Sebastian

Publication type:

Article

Principals about principal components in statistical genetics.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2200, doi. 10.1093/bib/bby081

By:

Abegaz, Fentaw;
Chaichoompu, Kridsadakorn;
Génin, Emmanuelle;
Fardo, David W;
König, Inke R;
John, Jestinah M Mahachie;
Steen, Kristel Van

Publication type:

Article

Polygenic approaches to detect gene–environment interactions when external information is unavailable.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2236, doi. 10.1093/bib/bby086

By:

Lin, Wan-Yu;
Huang, Ching-Chieh;
Liu, Yu-Li;
Tsai, Shih-Jen;
Kuo, Po-Hsiu

Publication type:

Article

PCA-based GRS analysis enhances the effectiveness for genetic correlation detection.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2291, doi. 10.1093/bib/bby075

By:

Zhao, Yan;
Ning, Yujie;
Zhang, Feng;
Ding, Miao;
Wen, Yan;
Shi, Liang;
Wang, Kunpeng;
Lu, Mengnan;
Sun, Jingyan;
Wu, Menglu;
Cheng, Bolun;
Ma, Mei;
Zhang, Lu;
Cheng, Shiqiang;
Shen, Hui;
Tian, Qing;
Guo, Xiong;
Deng, Hong-Wen

Publication type:

Article

Metabolomics technology and bioinformatics for precision medicine.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 1957, doi. 10.1093/bib/bbx170

By:

Azad, Rajeev K;
Shulaev, Vladimir

Publication type:

Article

Machine learning meets genome assembly.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2116, doi. 10.1093/bib/bby072

By:

Souza, Kleber Padovani de;
Setubal, João Carlos;
Carvalho, André Carlos Ponce de Leon F. de;
Oliveira, Guilherme;
Chateau, Annie;
Alves, Ronnie

Publication type:

Article

LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2009, doi. 10.1093/bib/bby065

By:

Han, Siyu;
Liang, Yanchun;
Ma, Qin;
Xu, Yangyi;
Zhang, Yu;
Du, Wei;
Wang, Cankun;
Li, Ying

Publication type:

Article

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2267, doi. 10.1093/bib/bby089

By:

Chen, Zhen;
Liu, Xuhan;
Li, Fuyi;
Li, Chen;
Marquez-Lago, Tatiana;
Leier, André;
Akutsu, Tatsuya;
Webb, Geoffrey I;
Xu, Dakang;
Smith, Alexander Ian;
Li, Lei;
Chou, Kuo-Chen;
Song, Jiangning

Publication type:

Article

Interpretation of differential gene expression results of RNA-seq data: review and integration.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2044, doi. 10.1093/bib/bby067

By:

McDermaid, Adam;
Monier, Brandon;
Zhao, Jing;
Liu, Bingqiang;
Ma, Qin

Publication type:

Article

Impact of similarity metrics on single-cell RNA-seq data clustering.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2316, doi. 10.1093/bib/bby076

By:

Kim, Taiyun;
Chen, Irene Rui;
Lin, Yingxin;
Wang, Andy Yi-Yang;
Yang, Jean Yee Hwa;
Yang, Pengyi

Publication type:

Article

An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2224, doi. 10.1093/bib/bby085

By:

Mallik, Saurav;
Odom, Gabriel J;
Gao, Zhen;
Gomez, Lissette;
Chen, Xi;
Wang, Lily

Publication type:

Article

Control principles for complex biological networks.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2253, doi. 10.1093/bib/bby088

By:

Li, Min;
Gao, Hao;
Wang, Jianxin;
Wu, Fang-Xiang

Publication type:

Article

Computational resources associating diseases with genotypes, phenotypes and exposures.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2098, doi. 10.1093/bib/bby071

By:

Zhang, Wenliang;
Zhang, Haiyue;
Yang, Huan;
Li, Miaoxin;
Xie, Zhi;
Li, Weizhong

Publication type:

Article

Computational determination of gene age and characterization of evolutionary dynamics in human.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2141, doi. 10.1093/bib/bby074

By:

Yin, Hongyan;
Li, Mengwei;
Xia, Lin;
He, Chaozu;
Zhang, Zhang

Publication type:

Article

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2185, doi. 10.1093/bib/bby079

By:

Zhang, Yanju;
Xie, Ruopeng;
Wang, Jiawei;
Leier, André;
Marquez-Lago, Tatiana T;
Akutsu, Tatsuya;
Webb, Geoffrey I;
Chou, Kuo-Chen;
Song, Jiangning

Publication type:

Article

Comprehensive comparative analysis of methods and software for identifying viral integrations.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2088, doi. 10.1093/bib/bby070

By:

Chen, Xun;
Kost, Jason;
Li, Dawei

Publication type:

Article

A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2055, doi. 10.1093/bib/bby068

By:

Brägelmann, Johannes;
Bermejo, Justo Lorenzo

Publication type:

Article

dbCID: a manually curated resource for exploring the driver indels in human cancer.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1925, doi. 10.1093/bib/bby059

By:

Yue, Zhenyu;
Zhao, Le;
Cheng, Na;
Yan, Hua;
Xia, Junfeng

Publication type:

Article

An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F<sub>2</sub>.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1913, doi. 10.1093/bib/bby058

By:

Wen, Yang-Jun;
Zhang, Ya-Wen;
Zhang, Jin;
Feng, Jian-Ying;
Dunwell, Jim M;
Zhang, Yuan-Ming

Publication type:

Article

Binding site matching in rational drug design: algorithms and applications.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2167, doi. 10.1093/bib/bby078

By:

Naderi, Misagh;
Lemoine, Jeffrey Mitchell;
Govindaraj, Rajiv Gandhi;
Kana, Omar Zade;
Feinstein, Wei Pan;
Brylinski, Michal

Publication type:

Article

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1878, doi. 10.1093/bib/bby061

By:

Rifaioglu, Ahmet Sureyya;
Atas, Heval;
Martin, Maria Jesus;
Cetin-Atalay, Rengul;
Atalay, Volkan;
Doğan, Tunca

Publication type:

Article

Corrigendum to: How trees allocate carbon for optimal growth: insight from a game-theoretic model.

Published in:: Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1956, doi. 10.1093/bib/bby060
Publication type:: Article

A brief history of bioinformatics.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 1981, doi. 10.1093/bib/bby063

By:

Gauthier, Jeff;
Vincent, Antony T;
Charette, Steve J;
Derome, Nicolas

Publication type:

Article

Breast cancer prognosis signature: linking risk stratification to disease subtypes.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2130, doi. 10.1093/bib/bby073

By:

Yu, Fulong;
Quan, Fei;
Xu, Jinyuan;
Zhang, Yan;
Xie, Yi;
Zhang, Jingyu;
Lan, Yujia;
Yuan, Huating;
Zhang, Hongyi;
Cheng, Shujun;
Xiao, Yun;
Li, Xia

Publication type:

Article

A practical guide for DNase-seq data analysis: from data management to common applications.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1865, doi. 10.1093/bib/bby057

By:

Liu, Yongjing;
Fu, Liangyu;
Kaufmann, Kerstin;
Chen, Dijun;
Chen, Ming

Publication type:

Article

ATAC-pipe: general analysis of genome-wide chromatin accessibility.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1934, doi. 10.1093/bib/bby056

By:

Zuo, Zuqi;
Jin, Yonghao;
Zhang, Wen;
Lu, Yichen;
Li, Bin;
Qu, Kun

Publication type:

Article

The small peptide world in long noncoding RNAs.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1853, doi. 10.1093/bib/bby055

By:

Choi, Seo-Won;
Kim, Hyun-Woo;
Nam, Jin-Wu

Publication type:

Article

Disease classification: from phenotypic similarity to integrative genomics and beyond.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1769, doi. 10.1093/bib/bby049

By:

Dozmorov, Mikhail G

Publication type:

Article

Function determinants of TET proteins: the arrangements of sequence motifs with specific codes.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1826, doi. 10.1093/bib/bby053

By:

Liu, Dongyang;
Li, Guangpeng;
Zuo, Yongchun

Publication type:

Article

Landscape of the long non-coding RNA transcriptome in human heart.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1812, doi. 10.1093/bib/bby052

By:

Jiang, Chunjie;
Ding, Na;
Li, Junyi;
Jin, Xiyun;
Li, Lili;
Pan, Tao;
Huo, Caiqin;
Li, Yongsheng;
Xu, Juan;
Li, Xia

Publication type:

Article

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1795, doi. 10.1093/bib/bby051

By:

Lightbody, Gaye;
Haberland, Valeriia;
Browne, Fiona;
Taggart, Laura;
Zheng, Huiru;
Parkes, Eileen;
Blayney, Jaine K

Publication type:

Article

Versatile interactions and bioinformatics analysis of noncoding RNAs.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1781, doi. 10.1093/bib/bby050

By:

Chen, Qi;
Meng, Xianwen;
Liao, Qi;
Chen, Ming

Publication type:

Article

Trends in the development of miRNA bioinformatics tools.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1836, doi. 10.1093/bib/bby054

By:

Chen, Liang;
Heikkinen, Liisa;
Wang, Changliang;
Yang, Yang;
Sun, Huiyan;
Wong, Garry

Publication type:

Article

Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1944, doi. 10.1093/bib/bby048

By:

Schmitt, Oliver;
Eipert, Peter;
Schwanke, Sebastian;
Lessmann, Felix;
Meinhardt, Jennifer;
Beier, Julia;
Kadir, Kanar;
Karnitzki, Adrian;
Sellner, Linda;
Klünker, Ann-Christin;
Ruß, Frauke;
Jenssen, Jörg

Publication type:

Article

Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1754, doi. 10.1093/bib/bby047

By:

Sulakhe, Dinanath;
D'Souza, Mark;
Wang, Sheng;
Balasubramanian, Sandhya;
Athri, Prashanth;
Xie, Bingqing;
Canzar, Stefan;
Agam, Gady;
Gilliam, T Conrad;
Maltsev, Natalia

Publication type:

Article

Evaluating the consistency of large-scale pharmacogenomic studies.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1734, doi. 10.1093/bib/bby046

By:

Rahman, Raziur;
Dhruba, Saugato Rahman;
Matlock, Kevin;
De-Niz, Carlos;
Ghosh, Souparno;
Pal, Ranadip

Publication type:

Article

Physiological RNA dynamics in RNA-Seq analysis.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1725, doi. 10.1093/bib/bby045

By:

Xu, Zhongneng;
Asakawa, Shuichi

Publication type:

Article

A comprehensive survey of models for dissecting local ancestry deconvolution in human genome.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1709, doi. 10.1093/bib/bby044

By:

Geza, Ephifania;
Mugo, Jacquiline;
Mulder, Nicola J;
Wonkam, Ambroise;
Chimusa, Emile R;
Mazandu, Gaston K

Publication type:

Article

In silico clinical trials: concepts and early adoptions.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1699, doi. 10.1093/bib/bby043

By:

Pappalardo, Francesco;
Russo, Giulia;
Tshinanu, Flora Musuamba;
Viceconti, Marco

Publication type:

Article

Microbial genomic island discovery, visualization and analysis.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1685, doi. 10.1093/bib/bby042

By:

Bertelli, Claire;
Tilley, Keith E;
Brinkman, Fiona S L

Publication type:

Article

Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1669, doi. 10.1093/bib/bby041

By:

Bao, Yu;
Marini, Simone;
Tamura, Takeyuki;
Kamada, Mayumi;
Maegawa, Shingo;
Hosokawa, Hiroshi;
Song, Jiangning;
Akutsu, Tatsuya

Publication type:

Article

A comparison of mechanistic signaling pathway activity analysis methods.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 5, p. 1655, doi. 10.1093/bib/bby040

By:

Amadoz, Alicia;
Hidalgo, Marta R;
Çubuk, Cankut;
Carbonell-Caballero, José;
Dopazo, Joaquín

Publication type:

Article