Subject: Briefings in Bioinformatics Table of Contents for January 2020 ------=_Part_1631261725.1581668930464 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Briefings in Bioinformatics *** Volume 21, Issue 1, 17 January 2020 Read this issue (https://academic.oup.com/bib/issue/21/1) ------------------------------ What research is making an impact in bioinformatics? Explore our collection of highly cited articles from Briefings in Bioinformatics. These articles are freely available until the end of 2019. Read the collection ------------------------------ ============================= Articles ============================Sequence clustering in bioinformatics: an empirical study Quan Zou, Gang Lin, Xingpeng Jiang, Xiangrong Liu, Xiangxiang Zeng (https://academic.oup.com/bib/article/21/1/1/5098604) CPPred-FL: a sequence-based predictor for large-scale identification of cell-penetrating peptides by feature representation learning Xiaoli Qiang, Chen Zhou, Xiucai Ye, Pu-feng Du, Ran Su (https://academic.oup.com/bib/article/21/1/11/5096827) Strategies for calibrating models of biology Mark N Read, Kieran Alden, Jon Timmis, Paul S Andrews (https://academic.oup.com/bib/article/21/1/24/5099477) Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data Sangsoo Lim, Sangseon Lee, Inuk Jung, Sungmin Rhee, Sun Kim (https://academic.oup.com/bib/article/21/1/36/5181542) MicroRNA-small molecule association identification: from experimental results to computational models Xing Chen, Na-Na Guan, Ya-Zhou Sun, Jian-Qiang Li, Jia Qu (https://academic.oup.com/bib/article/21/1/47/5122726) Human-like layout algorithms for signalling hypergraphs: outlining requirements Martin Siebenhaller, Sune S Nielsen, Fintan McGee, Irina Balaur, Charles Auffray (https://academic.oup.com/bib/article/21/1/62/5115270) The landscape of miRNA-related ceRNA networks for marking different renal cell carcinoma subtypes Liu Qin, Yanhong Liu, Menglong Li, Xuemei Pu, Yanzhi Guo (https://academic.oup.com/bib/article/21/1/73/5177804) Landscape of SNPs-mediated lncRNA structural variations and their implication in human complex diseases Hong Wang, Xiaoyan Lu, Fukun Chen, Yu Ding, Hewei Zheng (https://academic.oup.com/bib/article/21/1/85/5144269) The application of Hadoop in structural bioinformatics Jamie J Alnasir, Hugh P Shanahan (https://academic.oup.com/bib/article/21/1/96/5162997) Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms Leyi Wei, Jie Hu, Fuyi Li, Jiangning Song, Ran Su (https://academic.oup.com/bib/article/21/1/106/5152318) A comprehensive review of computational prediction of genome-wide features Tianlei Xu, Xiaoqi Zheng, Ben Li, Peng Jin, Zhaohui Qin (https://academic.oup.com/bib/article/21/1/120/5177808) Characteristics of plant circular RNAs Qinjie Chu, Panpan Bai, Xintian Zhu, Xingchen Zhang, Lingfeng Mao (https://academic.oup.com/bib/article/21/1/135/5164323) Dating admixture events is unsolved problem in multi-way admixed populations Emile R Chimusa, Joel Defo, Prisca K Thami, Denis Awany, Delesa D Mulisa (https://academic.oup.com/bib/article/21/1/144/5168590) Multilevel heterogeneous omics data integration with kernel fusion Haitao Yang, Hongyan Cao, Tao He, Tong Wang, Yuehua Cui (https://academic.oup.com/bib/article/21/1/156/5200557) Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment Chuan Dong, Yan-Ting Jin, Hong-Li Hua, Qing-Feng Wen, Sen Luo (https://academic.oup.com/bib/article/21/1/171/5200783) Network embedding in biomedical data science Chang Su, Jie Tong, Yongjun Zhu, Peng Cui, Fei Wang (https://academic.oup.com/bib/article/21/1/182/5228144) Fuzzy Petri nets for modelling of uncertain biological systems Fei Liu, Monika Heiner, David Gilbert (https://academic.oup.com/bib/article/21/1/198/5251018) Interactive visual analysis of drug'target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing Ziaurrehman Tanoli, Zaid Alam, Aleksandr Ianevski, Krister Wennerberg, Markus Vähä-Koskela (https://academic.oup.com/bib/article/21/1/211/5232987) Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures Jifan Shi, Andrew E Teschendorff, Weiyan Chen, Luonan Chen, Tiejun Li (https://academic.oup.com/bib/article/21/1/248/5115275) Algebraic shortcuts for leave-one-out cross-validation in supervised network inference Michiel Stock, Tapio Pahikkala, Antti Airola, Willem Waegeman, Bernard De Baets (https://academic.oup.com/bib/article/21/1/262/5124288) Copy number aberrations from Affymetrix SNP 6.0 genotyping data'how accurate are commonly used prediction approaches? Adriana Pitea, Ivan Kondofersky, Steffen Sass, Fabian J Theis, Nikola S Mueller (https://academic.oup.com/bib/article/21/1/272/5139664) Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power Chao Shen, Zhe Wang, Xiaojun Yao, Youyong Li, Tailong Lei (https://academic.oup.com/bib/article/21/1/282/5144987) HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search Bin Liu, Shuangyan Jiang, Quan Zou (https://academic.oup.com/bib/article/21/1/298/5150482) dbCPM: a manually curated database for exploring the cancer passenger mutations Zhenyu Yue, Le Zhao, Junfeng Xia (https://academic.oup.com/bib/article/21/1/309/5144624) AIMMS suite: a web server dedicated for prediction of drug resistance on protein mutation Feng-Xu Wu, Fan Wang, Jing-Fang Yang, Wen Jiang, Meng-Yao Wang (https://academic.oup.com/bib/article/21/1/318/5204135) gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population Dan Yao, Hainan Wu, Yuhua Chen, Wenguo Yang, Hua Gao (https://academic.oup.com/bib/article/21/1/329/5181553) Cancer-specific expression quantitative loci are affected by expression dysregulation Quanhu Sheng, David C Samuels, Hui Yu, Scott Ness, Ying-yong Zhao (https://academic.oup.com/bib/article/21/1/338/5194058) CytoPred: 7-gene pair metric for AML cytogenetic risk prediction Sameer Salunkhe, Naren Chandran, Pratik Chandrani, Amit Dutt, Shilpee Dutt (https://academic.oup.com/bib/article/21/1/348/5144166) Bioinformatics methodologies for coeliac disease and its comorbidities Eugenio Del Prete, Angelo Facchiano, Pietro Liò (https://academic.oup.com/bib/article/21/1/355/5164364) ------------------------------ This email alert does not include all articles within the issue. View complete issue (https://academic.oup.com/bib/issue/21/1) ------------------------------ Unsubscribe (http://cp20.com/unsubscribe) Manage email alerts (https://academic.oup.com/my-account/email-alerts) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK. Our Privacy Policy (http://global.oup.com/privacy) sets out how Oxford University Press handles your personal information. The content of this email is protected by copyright. Oxford University Press This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1631261725.1581668930464 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Explore our collection of highly cited articles from Briefings in Bioinformatics. These articles are freely available until the end of 2019.
Read the collection
 
 
 
 
 
 
Briefings in Bioinformatics  
Volume 21 Issue 1
 
January 2020
 
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Articles
 
 
 
Sequence clustering in bioinformatics: an empirical study 
 
Quan Zou; Gang Lin; Xingpeng Jiang ; Xiangrong Liu; Xiangxiang Zeng
 
 
CPPred-FL: a sequence-based predictor for large-scale identification of cell-penetrating peptides by feature representation learning 
 
Xiaoli Qiang; Chen Zhou; Xiucai Ye ; Pu-feng Du; Ran Su ...
 
 
Strategies for calibrating models of biology 
 
Mark N Read; Kieran Alden; Jon Timmis ; Paul S Andrews
 
 
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data 
 
Sangsoo Lim; Sangseon Lee; Inuk Jung ; Sungmin Rhee; Sun Kim
 
 
MicroRNA-small molecule association identification: from experimental results to computational models 
 
Xing Chen; Na-Na Guan; Ya-Zhou Sun ; Jian-Qiang Li; Jia Qu
 
 
Human-like layout algorithms for signalling hypergraphs: outlining requirements border= 
 
Martin Siebenhaller ; Sune S Nielsen; Fintan McGee; Irina Balaur; Charles Auffray ...
 
 
The landscape of miRNA-related ceRNA networks for marking different renal cell carcinoma subtypes 
 
Liu Qin; Yanhong Liu; Menglong Li ; Xuemei Pu; Yanzhi Guo
 
 
Landscape of SNPs-mediated lncRNA structural variations and their implication in human complex diseases 
 
Hong Wang; Xiaoyan Lu; Fukun Chen ; Yu Ding; Hewei Zheng ...
 
 
The application of Hadoop in structural bioinformatics 
 
Jamie J Alnasir; Hugh P Shanahan
 
 
Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms 
 
Leyi Wei; Jie Hu; Fuyi Li ; Jiangning Song; Ran Su ...
 
 
A comprehensive review of computational prediction of genome-wide features 
 
Tianlei Xu; Xiaoqi Zheng; Ben Li ; Peng Jin; Zhaohui Qin ...
 
 
Characteristics of plant circular RNAs 
 
Qinjie Chu; Panpan Bai; Xintian Zhu ; Xingchen Zhang; Lingfeng Mao ...
 
 
Dating admixture events is unsolved problem in multi-way admixed populations 
 
Emile R Chimusa; Joel Defo; Prisca K Thami ; Denis Awany; Delesa D Mulisa ...
 
 
Multilevel heterogeneous omics data integration with kernel fusion 
 
Haitao Yang; Hongyan Cao; Tao He ; Tong Wang; Yuehua Cui
 
 
Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment 
 
Chuan Dong; Yan-Ting Jin; Hong-Li Hua ; Qing-Feng Wen; Sen Luo ...
 
 
Network embedding in biomedical data science 
 
Chang Su; Jie Tong; Yongjun Zhu ; Peng Cui; Fei Wang
 
 
Fuzzy Petri nets for modelling of uncertain biological systems 
 
Fei Liu; Monika Heiner; David Gilbert
 
 
Interactive visual analysis of drug'target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing border= 
 
Ziaurrehman Tanoli ; Zaid Alam; Aleksandr Ianevski; Krister Wennerberg; Markus Vähä-Koskela ...
 
 
Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures border= 
 
Jifan Shi ; Andrew E Teschendorff; Weiyan Chen; Luonan Chen; Tiejun Li
 
 
Algebraic shortcuts for leave-one-out cross-validation in supervised network inference 
 
Michiel Stock; Tapio Pahikkala; Antti Airola ; Willem Waegeman; Bernard De Baets
 
 
Copy number aberrations from Affymetrix SNP 6.0 genotyping data'how accurate are commonly used prediction approaches? border= 
 
Adriana Pitea ; Ivan Kondofersky; Steffen Sass; Fabian J Theis; Nikola S Mueller ...
 
 
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power 
 
Chao Shen; Zhe Wang; Xiaojun Yao ; Youyong Li; Tailong Lei ...
 
 
HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search 
 
Bin Liu; Shuangyan Jiang; Quan Zou
 
 
dbCPM: a manually curated database for exploring the cancer passenger mutations 
 
Zhenyu Yue; Le Zhao; Junfeng Xia
 
 
AIMMS suite: a web server dedicated for prediction of drug resistance on protein mutation 
 
Feng-Xu Wu; Fan Wang; Jing-Fang Yang ; Wen Jiang; Meng-Yao Wang ...
 
 
gm RAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population border= 
 
Dan Yao ; Hainan Wu; Yuhua Chen; Wenguo Yang; Hua Gao ...
 
 
Cancer-specific expression quantitative loci are affected by expression dysregulation 
 
Quanhu Sheng; David C Samuels; Hui Yu ; Scott Ness; Ying-yong Zhao ...
 
 
CytoPred: 7-gene pair metric for AML cytogenetic risk prediction 
 
Sameer Salunkhe; Naren Chandran; Pratik Chandrani ; Amit Dutt; Shilpee Dutt
 
 
Bioinformatics methodologies for coeliac disease and its comorbidities 
 
Eugenio Del Prete; Angelo Facchiano; Pietro Liò
 
 
 
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