Subject: Briefings in Bioinformatics Table of Contents for November 2019 ------=_Part_1701346876.1579024692431 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Briefings in Bioinformatics *** Volume 20, Issue 6, 27 November 2019 Read this issue (https://academic.oup.com/bib/issue/20/6) ------------------------------ 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 ============================Metabolomics technology and bioinformatics for precision medicine Rajeev K Azad, Vladimir Shulaev (https://academic.oup.com/bib/article/20/6/1957/4785947) A review of metrics measuring dissimilarity for rooted phylogenetic networks Juan Wang, Maozu Guo (https://academic.oup.com/bib/article/20/6/1972/5055373) A brief history of bioinformatics Jeff Gauthier, Antony T Vincent, Steve J Charette, Nicolas Derome (https://academic.oup.com/bib/article/20/6/1981/5066445) Sequencing era methods for identifying signatures of selection in the genome Clare Horscroft, Sarah Ennis, Reuben J Pengelly, Timothy J Sluckin, Andrew Collins (https://academic.oup.com/bib/article/20/6/1997/5057989) LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang (https://academic.oup.com/bib/article/20/6/2009/5062950) Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka (https://academic.oup.com/bib/article/20/6/2028/5066172) Interpretation of differential gene expression results of RNA-seq data: review and integration Adam McDermaid, Brandon Monier, Jing Zhao, Bingqiang Liu, Qin Ma (https://academic.oup.com/bib/article/20/6/2044/5066173) A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets Johannes Brägelmann, Justo Lorenzo Bermejo (https://academic.oup.com/bib/article/20/6/2055/5066710) Review and comparative assessment of similarity-based methods for prediction of drug--protein interactions in the druggable human proteome Chen Wang, Lukasz Kurgan (https://academic.oup.com/bib/article/20/6/2066/5066711) Comprehensive comparative analysis of methods and software for identifying viral integrations Xun Chen, Jason Kost, Dawei Li (https://academic.oup.com/bib/article/20/6/2088/5066709) Computational resources associating diseases with genotypes, phenotypes and exposures Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie (https://academic.oup.com/bib/article/20/6/2098/5067517) Machine learning meets genome assembly Kleber Padovani de Souza, Joao Carlos Setubal, André Carlos Ponce de Leon F. de Carvalho, Guilherme Oliveira, Annie Chateau (https://academic.oup.com/bib/article/20/6/2116/5074612) Breast cancer prognosis signature: linking risk stratification to disease subtypes Fulong Yu, Fei Quan, Jinyuan Xu, Yan Zhang, Yi Xie (https://academic.oup.com/bib/article/20/6/2130/5090083) Computational determination of gene age and characterization of evolutionary dynamics in human Hongyan Yin, Mengwei Li, Lin Xia, Chaozu He, Zhang Zhang (https://academic.oup.com/bib/article/20/6/2141/5089936) Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods Fuyi Li, Yanan Wang, Chen Li, Tatiana T Marquez-Lago, André Leier (https://academic.oup.com/bib/article/20/6/2150/5078120) Binding site matching in rational drug design: algorithms and applications Misagh Naderi, Jeffrey Mitchell Lemoine, Rajiv Gandhi Govindaraj, Omar Zade Kana, Wei Pan Feinstein (https://academic.oup.com/bib/article/20/6/2167/5087973) Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T Marquez-Lago (https://academic.oup.com/bib/article/20/6/2185/5078519) Principals about principal components in statistical genetics Fentaw Abegaz, Kridsadakorn Chaichoompu, Emmanuelle Génin, David W Fardo, Inke R König (https://academic.oup.com/bib/article/20/6/2200/5095727) Quick approximation of threshold values for genome-wide association studies Zhiyu Hao, Li Jiang, Jin Gao, Jinhua Ye, Jingli Zhao (https://academic.oup.com/bib/article/20/6/2217/5093777) An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays Saurav Mallik, Gabriel J Odom, Zhen Gao, Lissette Gomez, Xi Chen (https://academic.oup.com/bib/article/20/6/2224/5096828) Polygenic approaches to detect gene--environment interactions when external information is unavailable Wan-Yu Lin, Ching-Chieh Huang, Yu-Li Liu, Shih-Jen Tsai, Po-Hsiu Kuo (https://academic.oup.com/bib/article/20/6/2236/5091280) Control principles for complex biological networks Min Li, Hao Gao, Jianxin Wang, Fang-Xiang Wu (https://academic.oup.com/bib/article/20/6/2253/5099476) Large-scale comparative assessment of computational predictors for lysine post-translational modification sites Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana Marquez-Lago (https://academic.oup.com/bib/article/20/6/2267/5106678) PCA-based GRS analysis enhances the effectiveness for genetic correlation detection Yan Zhao, Yujie Ning, Feng Zhang, Miao Ding, Yan Wen (https://academic.oup.com/bib/article/20/6/2291/5085925) Protein--peptide docking using CABS-dock and contact information Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik (https://academic.oup.com/bib/article/20/6/2299/5095729) Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations Meng Zou, Rui Jin, Kin Fai Au (https://academic.oup.com/bib/article/20/6/2306/5091279) Impact of similarity metrics on single-cell RNA-seq data clustering Taiyun Kim, Irene Rui Chen, Yingxin Lin, Andy Yi-Yang Wang, Jean Yee Hwa Yang (https://academic.oup.com/bib/article/20/6/2316/5077112) TRCirc: a resource for transcriptional regulation information of circRNAs Zhidong Tang, Xuecang Li, Jianmei Zhao, Fengcui Qian, Chenchen Feng (https://academic.oup.com/bib/article/20/6/2327/5089935) 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_1701346876.1579024692431 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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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
 
 
 
 
 
 
Briefings in Bioinformatics  
Volume 20 Issue 6
 
November 2019
 
button-issue.png
 
 
Articles
 
 
 
Metabolomics technology and bioinformatics for precision medicine 
 
Rajeev K Azad; Vladimir Shulaev
 
 
A review of metrics measuring dissimilarity for rooted phylogenetic networks 
 
Juan Wang; Maozu Guo
 
 
A brief history of bioinformatics 
 
Jeff Gauthier; Antony T Vincent; Steve J Charette ; Nicolas Derome
 
 
Sequencing era methods for identifying signatures of selection in the genome 
 
Clare Horscroft; Sarah Ennis; Reuben J Pengelly ; Timothy J Sluckin; Andrew Collins
 
 
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property border= 
 
Siyu Han ; Yanchun Liang; Qin Ma; Yangyi Xu; Yu Zhang ...
 
 
Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches border= 
 
Dai Hai Nguyen ; Canh Hao Nguyen; Hiroshi Mamitsuka
 
 
Interpretation of differential gene expression results of RNA-seq data: review and integration 
 
Adam McDermaid; Brandon Monier; Jing Zhao ; Bingqiang Liu; Qin Ma
 
 
A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets border= 
 
Johannes Brägelmann ; Justo Lorenzo Bermejo
 
 
Review and comparative assessment of similarity-based methods for prediction of drug'protein interactions in the druggable human proteome 
 
Chen Wang; Lukasz Kurgan
 
 
Comprehensive comparative analysis of methods and software for identifying viral integrations 
 
Xun Chen; Jason Kost; Dawei Li
 
 
Computational resources associating diseases with genotypes, phenotypes and exposures border= 
 
Wenliang Zhang ; Haiyue Zhang; Huan Yang; Miaoxin Li; Zhi Xie ...
 
 
Machine learning meets genome assembly 
 
Kleber Padovani de Souza; João Carlos Setubal; André Carlos Ponce de Leon F. de Carvalho ; Guilherme Oliveira; Annie Chateau ...
 
 
Breast cancer prognosis signature: linking risk stratification to disease subtypes 
 
Fulong Yu; Fei Quan; Jinyuan Xu ; Yan Zhang; Yi Xie ...
 
 
Computational determination of gene age and characterization of evolutionary dynamics in human 
 
Hongyan Yin; Mengwei Li; Lin Xia ; Chaozu He; Zhang Zhang
 
 
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods 
 
Fuyi Li; Yanan Wang; Chen Li ; Tatiana T Marquez-Lago; André Leier ...
 
 
Binding site matching in rational drug design: algorithms and applications 
 
Misagh Naderi; Jeffrey Mitchell Lemoine; Rajiv Gandhi Govindaraj ; Omar Zade Kana; Wei Pan Feinstein ...
 
 
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework 
 
Yanju Zhang; Ruopeng Xie; Jiawei Wang ; André Leier; Tatiana T Marquez-Lago ...
 
 
Principals about principal components in statistical genetics 
 
Fentaw Abegaz; Kridsadakorn Chaichoompu; Emmanuelle Génin ; David W Fardo; Inke R König ...
 
 
Quick approximation of threshold values for genome-wide association studies 
 
Zhiyu Hao; Li Jiang; Jin Gao ; Jinhua Ye; Jingli Zhao ...
 
 
An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays border= 
 
Saurav Mallik ; Gabriel J Odom; Zhen Gao; Lissette Gomez; Xi Chen ...
 
 
Polygenic approaches to detect gene'environment interactions when external information is unavailable border= 
 
Wan-Yu Lin ; Ching-Chieh Huang; Yu-Li Liu; Shih-Jen Tsai; Po-Hsiu Kuo
 
 
Control principles for complex biological networks 
 
Min Li; Hao Gao; Jianxin Wang ; Fang-Xiang Wu
 
 
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites 
 
Zhen Chen; Xuhan Liu; Fuyi Li ; Chen Li; Tatiana Marquez-Lago ...
 
 
PCA-based GRS analysis enhances the effectiveness for genetic correlation detection 
 
Yan Zhao; Yujie Ning; Feng Zhang ; Miao Ding; Yan Wen ...
 
 
Protein'peptide docking using CABS-dock and contact information border= 
 
Maciej Blaszczyk ; Maciej Pawel Ciemny; Andrzej Kolinski; Mateusz Kurcinski; Sebastian Kmiecik
 
 
Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations border= 
 
Meng Zou ; Rui Jin; Kin Fai Au
 
 
Impact of similarity metrics on single-cell RNA-seq data clustering 
 
Taiyun Kim; Irene Rui Chen; Yingxin Lin ; Andy Yi-Yang Wang; Jean Yee Hwa Yang ...
 
 
TRCirc: a resource for transcriptional regulation information of circRNAs 
 
Zhidong Tang; Xuecang Li; Jianmei Zhao ; Fengcui Qian; Chenchen Feng ...
 
 
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