Subject: Briefings in Bioinformatics Table of Contents for May 2020 ------=_Part_2006950146.1590187812367 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Briefings in Bioinformatics *** Volume 21, Issue 3, 21 May 2020 Read this issue (https://academic.oup.com/bib/issue/21/3) ============================= Articles ============================Optimal selection of genetic variants for adjustment of population stratification in European association studies Regina Brinster, Dominique Scherer, Justo Lorenzo Bermejo (https://academic.oup.com/bib/article/21/3/753/5373123) Evaluation of drug efficacy based on the spatial position comparison of drug'target interaction centers Yu Ding, Hong Wang, Hewei Zheng, Lianzong Wang, Guosi Zhang (https://academic.oup.com/bib/article/21/3/762/5373124) Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences Ziye Wang, Ying Wang, Jed A Fuhrman, Fengzhu Sun, Shanfeng Zhu (https://academic.oup.com/bib/article/21/3/777/5371422) Validation strategies for target prediction methods Neann Mathai, Ya Chen, Johannes Kirchmair (https://academic.oup.com/bib/article/21/3/791/5428023) Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes Fabio Fabris, Daniel Palmer, Joao Pedro de Magalhaes, Alex A Freitas (https://academic.oup.com/bib/article/21/3/803/5380425) Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications Zhongjie Liang, Gennady M Verkhivker, Guang Hu (https://academic.oup.com/bib/article/21/3/815/5393244) Shaping the nebulous enhancer in the era of high-throughput assays and genome editing Edwin Yu-Kiu Ho, Qin Cao, Mengting Gu, Ricky Wai-Lun Chan, Qiong Wu (https://academic.oup.com/bib/article/21/3/836/5381766) Comparison of haplotype-based tests for detecting gene'environment interactions with rare variants Charalampos Papachristou, Swati Biswas (https://academic.oup.com/bib/article/21/3/851/5475052) MicroRNAs and nervous system diseases: network insights and computational challenges Jianjian Wang, Yuze Cao, Xiaoyu Lu, Tianfeng Wang, Shuang Li (https://academic.oup.com/bib/article/21/3/863/5424156) Molecular Biology Information Service: an innovative medical library-based bioinformatics support service for biomedical researchers Ansuman Chattopadhyay, Carrie L Iwema, Barbara A Epstein, Adrian V Lee, Arthur S Levine (https://academic.oup.com/bib/article/21/3/876/5424165) 100 Years of evolving gene'disease complexities and scientific debutants Saman Zeeshan, Ruoyun Xiong, Bruce T Liang, Zeeshan Ahmed (https://academic.oup.com/bib/article/21/3/885/5436939) DNA methylation analysis in plants: review of computational tools and future perspectives Jimmy Omony, Thomas Nussbaumer, Ruben Gutzat (https://academic.oup.com/bib/article/21/3/906/5432309) Graph convolutional networks for computational drug development and discovery Mengying Sun, Sendong Zhao, Coryandar Gilvary, Olivier Elemento, Jiayu Zhou (https://academic.oup.com/bib/article/21/3/919/5498046) Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives Charles Vesteghem, Rasmus Froberg Brøndum, Mads Sønderkær, Mia Sommer, Alexander Schmitz (https://academic.oup.com/bib/article/21/3/936/5522017) Transcription factors'DNA interactions in rice: identification and verification Zijie Shen, Yuan Lin, Quan Zou (https://academic.oup.com/bib/article/21/3/946/5479606) A comprehensive overview of oncogenic pathways in human cancer Feng Li, Tan Wu, Yanjun Xu, Qun Dong, Jing Xiao (https://academic.oup.com/bib/article/21/3/957/5489890) Comparison and integration of computational methods for deleterious synonymous mutation prediction Na Cheng, Menglu Li, Le Zhao, Bo Zhang, Yuhua Yang (https://academic.oup.com/bib/article/21/3/970/5498048) Evaluation of different computational methods on 5-methylcytosine sites identification Hao Lv, Zi-Mei Zhang, Shi-Hao Li, Jiu-Xin Tan, Wei Chen (https://academic.oup.com/bib/article/21/3/982/5510088) ============================= Problem Solving Protocol ============================Meta-GDBP: a high-level stacked regression model to improve anticancer drug response prediction Ran Su, Xinyi Liu, Guobao Xiao, Leyi Wei (https://academic.oup.com/bib/article/21/3/996/5373125) Platform-independent approach for cancer detection from gene expression profiles of peripheral blood cells Yadong Yang, Tao Zhang, Rudan Xiao, Xiaopeng Hao, Huiqiang Zhang (https://academic.oup.com/bib/article/21/3/1006/5382262) Identifying psychiatric disorder-associated gut microbiota using microbiota-related gene set enrichment analysis Shiqiang Cheng, Bei Han, Miao Ding, Yan Wen, Mei Ma (https://academic.oup.com/bib/article/21/3/1016/5424164) Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data Zhijie Han, Weiwei Xue, Lin Tao, Yan Lou, Yunqing Qiu (https://academic.oup.com/bib/article/21/3/1023/5474909) A feature-based approach to predict hot spots in protein'DNA binding interfaces Sijia Zhang, Le Zhao, Chun-Hou Zheng, Junfeng Xia (https://academic.oup.com/bib/article/21/3/1038/5424984) iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T Marquez-Lago, André Leier (https://academic.oup.com/bib/article/21/3/1047/5475015) Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data Qingxia Yang, Bo Li, Jing Tang, Xuejiao Cui, Yunxia Wang (https://academic.oup.com/bib/article/21/3/1058/5510089) PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact Fuyi Li, Cunshuo Fan, Tatiana T Marquez-Lago, André Leier, Jerico Revote (https://academic.oup.com/bib/article/21/3/1069/5510293) Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas Ji Zhang, Meige Guan, Qianliang Wang, Jiajun Zhang, Tianshou Zhou (https://academic.oup.com/bib/article/21/3/1080/5475028) ============================= Case Study ============================Characterization and identification of antimicrobial peptides with different functional activities Chia-Ru Chung, Ting-Rung Kuo, Li-Ching Wu, Tzong-Yi Lee, Jorng-Tzong Horng (https://academic.oup.com/bib/article/21/3/1098/5498047) ============================= Letter to Editor ============================In silico signaling modeling to understand cancer pathways and treatment responses Meik Kunz, Julian Jeromin, Maximilian Fuchs, Jan Christoph, Giulia Veronesi (https://academic.oup.com/bib/article/21/3/1115/5450331) ============================= Corrigendum ============================Corrigendum to: Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data (https://academic.oup.com/bib/article/21/3/1118/5232442) 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_2006950146.1590187812367 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Briefings in Bioinformatics  
Volume 21 Issue 3
 
May 2020
 
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Articles
 
 
 
Optimal selection of genetic variants for adjustment of population stratification in European association studies 
 
Regina Brinster; Dominique Scherer; Justo Lorenzo Bermejo
 
 
Evaluation of drug efficacy based on the spatial position comparison of drug'target interaction centers 
 
Yu Ding; Hong Wang; Hewei Zheng ; Lianzong Wang; Guosi Zhang ...
 
 
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences 
 
Ziye Wang; Ying Wang; Jed A Fuhrman ; Fengzhu Sun; Shanfeng Zhu
 
 
Validation strategies for target prediction methods border=  
 
Neann Mathai; Ya Chen; Johannes Kirchmair
 
 
Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes 
 
Fabio Fabris; Daniel Palmer; João Pedro de Magalhães ; Alex A Freitas
 
 
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications  
 
Zhongjie Liang; Gennady M Verkhivker; Guang Hu
 
 
Shaping the nebulous enhancer in the era of high-throughput assays and genome editing 
 
Edwin Yu-Kiu Ho; Qin Cao; Mengting Gu ; Ricky Wai-Lun Chan; Qiong Wu ...
 
 
Comparison of haplotype-based tests for detecting gene'environment interactions with rare variants 
 
Charalampos Papachristou; Swati Biswas
 
 
MicroRNAs and nervous system diseases: network insights and computational challenges 
 
Jianjian Wang; Yuze Cao; Xiaoyu Lu ; Tianfeng Wang; Shuang Li ...
 
 
Molecular Biology Information Service: an innovative medical library-based bioinformatics support service for biomedical researchers 
 
Ansuman Chattopadhyay; Carrie L Iwema; Barbara A Epstein ; Adrian V Lee; Arthur S Levine
 
 
100 Years of evolving gene'disease complexities and scientific debutants 
 
Saman Zeeshan; Ruoyun Xiong; Bruce T Liang ; Zeeshan Ahmed
 
 
DNA methylation analysis in plants: review of computational tools and future perspectives 
 
Jimmy Omony; Thomas Nussbaumer; Ruben Gutzat
 
 
Graph convolutional networks for computational drug development and discovery 
 
Mengying Sun; Sendong Zhao; Coryandar Gilvary ; Olivier Elemento; Jiayu Zhou ...
 
 
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives border= 
 
Charles Vesteghem ; Rasmus Froberg Brøndum; Mads Sønderkær; Mia Sommer; Alexander Schmitz ...
 
 
Transcription factors'DNA interactions in rice: identification and verification 
 
Zijie Shen; Yuan Lin; Quan Zou
 
 
A comprehensive overview of oncogenic pathways in human cancer 
 
Feng Li; Tan Wu; Yanjun Xu ; Qun Dong; Jing Xiao ...
 
 
Comparison and integration of computational methods for deleterious synonymous mutation prediction 
 
Na Cheng; Menglu Li; Le Zhao ; Bo Zhang; Yuhua Yang ...
 
 
Evaluation of different computational methods on 5-methylcytosine sites identification 
 
Hao Lv; Zi-Mei Zhang; Shi-Hao Li ; Jiu-Xin Tan; Wei Chen ...
 
 
 
Problem Solving Protocol
 
 
 
Meta-GDBP: a high-level stacked regression model to improve anticancer drug response prediction 
 
Ran Su; Xinyi Liu; Guobao Xiao ; Leyi Wei
 
 
Platform-independent approach for cancer detection from gene expression profiles of peripheral blood cells 
 
Yadong Yang; Tao Zhang; Rudan Xiao ; Xiaopeng Hao; Huiqiang Zhang ...
 
 
Identifying psychiatric disorder-associated gut microbiota using microbiota-related gene set enrichment analysis 
 
Shiqiang Cheng; Bei Han; Miao Ding ; Yan Wen; Mei Ma ...
 
 
Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data 
 
Zhijie Han; Weiwei Xue; Lin Tao ; Yan Lou; Yunqing Qiu ...
 
 
A feature-based approach to predict hot spots in protein'DNA binding interfaces 
 
Sijia Zhang; Le Zhao; Chun-Hou Zheng ; Junfeng Xia
 
 
iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data 
 
Zhen Chen; Pei Zhao; Fuyi Li ; Tatiana T Marquez-Lago; André Leier ...
 
 
Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data 
 
Qingxia Yang; Bo Li; Jing Tang ; Xuejiao Cui; Yunxia Wang ...
 
 
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact 
 
Fuyi Li; Cunshuo Fan; Tatiana T Marquez-Lago ; André Leier; Jerico Revote ...
 
 
Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas 
 
Ji Zhang; Meige Guan; Qianliang Wang ; Jiajun Zhang; Tianshou Zhou ...
 
 
 
Case Study
 
 
 
Characterization and identification of antimicrobial peptides with different functional activities 
 
Chia-Ru Chung; Ting-Rung Kuo; Li-Ching Wu ; Tzong-Yi Lee; Jorng-Tzong Horng
 
 
 
Letter to Editor
 
 
 
In silico signaling modeling to understand cancer pathways and treatment responses 
 
Meik Kunz; Julian Jeromin; Maximilian Fuchs ; Jan Christoph; Giulia Veronesi ...
 
 
 
Corrigendum
 
 
 
Corrigendum to: Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data 
 
 
 
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