Subject: Briefings in Bioinformatics Table of Contents for September 2019 ------=_Part_2055333530.1576974155515 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Briefings in Bioinformatics *** Volume 20, Issue 5, 27 September 2019 Read this issue (https://academic.oup.com/bib/issue/20/5) ------------------------------ 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 ------------------------------ ============================= Review Articles ============================Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications Shaoping Shi, Lina Wang, Man Cao, Guodong Chen, Jialin Yu (https://academic.oup.com/bib/article/20/5/1597/4999248) Predicting novel microRNA: a comprehensive comparison of machine learning approaches Georgina Stegmayer, Leandro E Di Persia, Mariano Rubiolo, Matias Gerard, Milton Pividori (https://academic.oup.com/bib/article/20/5/1607/5001762) Survey of miRNA-miRNA cooperative regulation principles across cancer types Tingting Shao, Guangjuan Wang, Hong Chen, Yunjin Xie, Xiyun Jin (https://academic.oup.com/bib/article/20/5/1621/5004391) Regulatory variants: from detection to predicting impact Elena Rojano, Pedro Seoane, Juan A G Ranea, James R Perkins (https://academic.oup.com/bib/article/20/5/1639/5035219) A comparison of mechanistic signaling pathway activity analysis methods Alicia Amadoz, Marta R Hidalgo, Cankut Çubuk, José Carbonell-Caballero, Joaquín Dopazo (https://academic.oup.com/bib/article/20/5/1655/5032570) Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa (https://academic.oup.com/bib/article/20/5/1669/5026393) Microbial genomic island discovery, visualization and analysis Claire Bertelli, Keith E Tilley, Fiona S L Brinkman (https://academic.oup.com/bib/article/20/5/1685/5032564) In silico clinical trials: concepts and early adoptions Francesco Pappalardo, Giulia Russo, Flora Musuamba Tshinanu, Marco Viceconti (https://academic.oup.com/bib/article/20/5/1699/5032454) A comprehensive survey of models for dissecting local ancestry deconvolution in human genome Ephifania Geza, Jacquiline Mugo, Nicola J Mulder, Ambroise Wonkam, Emile R Chimusa (https://academic.oup.com/bib/article/20/5/1709/5047382) Physiological RNA dynamics in RNA-Seq analysis Zhongneng Xu, Shuichi Asakawa (https://academic.oup.com/bib/article/20/5/1725/5047383) Evaluating the consistency of large-scale pharmacogenomic studies Raziur Rahman, Saugato Rahman Dhruba, Kevin Matlock, Carlos De-Niz, Souparno Ghosh (https://academic.oup.com/bib/article/20/5/1734/5034074) Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources Dinanath Sulakhe, Mark D'Souza, Sheng Wang, Sandhya Balasubramanian, Prashanth Athri (https://academic.oup.com/bib/article/20/5/1754/5042182) Disease classification: from phenotypic similarity to integrative genomics and beyond Mikhail G Dozmorov (https://academic.oup.com/bib/article/20/5/1769/5043113) Versatile interactions and bioinformatics analysis of noncoding RNAs Qi Chen, Xianwen Meng, Qi Liao, Ming Chen (https://academic.oup.com/bib/article/20/5/1781/5043119) Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura Taggart, Huiru Zheng (https://academic.oup.com/bib/article/20/5/1795/5062275) Landscape of the long non-coding RNA transcriptome in human heart Chunjie Jiang, Na Ding, Junyi Li, Xiyun Jin, Lili Li (https://academic.oup.com/bib/article/20/5/1812/5043120) Function determinants of TET proteins: the arrangements of sequence motifs with specific codes Dongyang Liu, Guangpeng Li, Yongchun Zuo (https://academic.oup.com/bib/article/20/5/1826/5045641) Trends in the development of miRNA bioinformatics tools Liang Chen, Liisa Heikkinen, Changliang Wang, Yang Yang, Huiyan Sun (https://academic.oup.com/bib/article/20/5/1836/5047127) The small peptide world in long noncoding RNAs Seo-Won Choi, Hyun-Woo Kim, Jin-Wu Nam (https://academic.oup.com/bib/article/20/5/1853/5047384) A practical guide for DNase-seq data analysis: from data management to common applications Yongjing Liu, Liangyu Fu, Kerstin Kaufmann, Dijun Chen, Ming Chen (https://academic.oup.com/bib/article/20/5/1865/5053117) Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases Ahmet Sureyya Rifaioglu, Heval Atas, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay (https://academic.oup.com/bib/article/20/5/1878/5062947) ============================= Problem solving protocol ============================An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2 Yang-Jun Wen, Ya-Wen Zhang, Jin Zhang, Jian-Ying Feng, Jim M Dunwell (https://academic.oup.com/bib/article/20/5/1913/5055834) dbCID: a manually curated resource for exploring the driver indels in human cancer Zhenyu Yue, Le Zhao, Na Cheng, Hua Yan, Junfeng Xia (https://academic.oup.com/bib/article/20/5/1925/5054736) ATAC-pipe: general analysis of genome-wide chromatin accessibility Zuqi Zuo, Yonghao Jin, Wen Zhang, Yichen Lu, Bin Li (https://academic.oup.com/bib/article/20/5/1934/5047123) ============================= Case Study ============================Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity Oliver Schmitt, Peter Eipert, Sebastian Schwanke, Felix Lessmann, Jennifer Meinhardt (https://academic.oup.com/bib/article/20/5/1944/5036112) ============================= Corrigendum ============================Corrigendum to: How trees allocate carbon for optimal growth: insight from a game-theoretic model (https://academic.oup.com/bib/article/20/5/1956/5047385) 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_2055333530.1576974155515 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
oxford_logo.jpg
 
 
 
 
New issue alert
 
 
 
 
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 5
 
September 2019
 
button-issue.png
 
 
Review Articles
 
 
 
Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications 
 
Shaoping Shi; Lina Wang; Man Cao ; Guodong Chen; Jialin Yu
 
 
Predicting novel microRNA: a comprehensive comparison of machine learning approaches 
 
Georgina Stegmayer; Leandro E Di Persia; Mariano Rubiolo ; Matias Gerard; Milton Pividori ...
 
 
Survey of miRNA-miRNA cooperative regulation principles across cancer types 
 
Tingting Shao; Guangjuan Wang; Hong Chen ; Yunjin Xie; Xiyun Jin ...
 
 
Regulatory variants: from detection to predicting impact border=  
 
Elena Rojano; Pedro Seoane; Juan A G Ranea; James R Perkins
 
 
A comparison of mechanistic signaling pathway activity analysis methods border= 
 
Alicia Amadoz ; Marta R Hidalgo; Cankut Çubuk; José Carbonell-Caballero; Joaquín Dopazo
 
 
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features border= 
 
Yu Bao ; Simone Marini; Takeyuki Tamura; Mayumi Kamada; Shingo Maegawa ...
 
 
Microbial genomic island discovery, visualization and analysis border= 
 
Claire Bertelli ; Keith E Tilley; Fiona S L Brinkman
 
 
In silico clinical trials: concepts and early adoptions 
 
Francesco Pappalardo; Giulia Russo; Flora Musuamba Tshinanu ; Marco Viceconti
 
 
A comprehensive survey of models for dissecting local ancestry deconvolution in human genome 
 
Ephifania Geza; Jacquiline Mugo; Nicola J Mulder ; Ambroise Wonkam; Emile R Chimusa ...
 
 
Physiological RNA dynamics in RNA-Seq analysis 
 
Zhongneng Xu; Shuichi Asakawa
 
 
Evaluating the consistency of large-scale pharmacogenomic studies 
 
Raziur Rahman; Saugato Rahman Dhruba; Kevin Matlock ; Carlos De-Niz; Souparno Ghosh ...
 
 
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources 
 
Dinanath Sulakhe; Mark D'Souza; Sheng Wang ; Sandhya Balasubramanian; Prashanth Athri ...
 
 
Disease classification: from phenotypic similarity to integrative genomics and beyond 
 
Mikhail G Dozmorov
 
 
Versatile interactions and bioinformatics analysis of noncoding RNAs 
 
Qi Chen; Xianwen Meng; Qi Liao ; Ming Chen
 
 
Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application border= 
 
Gaye Lightbody ; Valeriia Haberland; Fiona Browne; Laura Taggart; Huiru Zheng ...
 
 
Landscape of the long non-coding RNA transcriptome in human heart 
 
Chunjie Jiang; Na Ding; Junyi Li ; Xiyun Jin; Lili Li ...
 
 
Function determinants of TET proteins: the arrangements of sequence motifs with specific codes 
 
Dongyang Liu; Guangpeng Li; Yongchun Zuo
 
 
Trends in the development of miRNA bioinformatics tools border=  
 
Liang Chen; Liisa Heikkinen; Changliang Wang; Yang Yang; Huiyan Sun ...
 
 
The small peptide world in long noncoding RNAs border=  
 
Seo-Won Choi; Hyun-Woo Kim; Jin-Wu Nam
 
 
A practical guide for DNase-seq data analysis: from data management to common applications 
 
Yongjing Liu; Liangyu Fu; Kerstin Kaufmann ; Dijun Chen; Ming Chen
 
 
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases border= 
 
Ahmet Sureyya Rifaioglu; Heval Atas; Maria Jesus Martin; Rengul Cetin-Atalay; Volkan Atalay ...
 
 
 
Problem solving protocol
 
 
 
An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2  border= 
 
Yang-Jun Wen; Ya-Wen Zhang ; Jin Zhang; Jian-Ying Feng; Jim M Dunwell ...
 
 
dbCID: a manually curated resource for exploring the driver indels in human cancer 
 
Zhenyu Yue; Le Zhao; Na Cheng ; Hua Yan; Junfeng Xia
 
 
ATAC-pipe: general analysis of genome-wide chromatin accessibility 
 
Zuqi Zuo; Yonghao Jin; Wen Zhang ; Yichen Lu; Bin Li ...
 
 
 
Case Study
 
 
 
Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity 
 
Oliver Schmitt; Peter Eipert; Sebastian Schwanke ; Felix Lessmann; Jennifer Meinhardt ...
 
 
 
Corrigendum
 
 
 
Corrigendum to: How trees allocate carbon for optimal growth: insight from a game-theoretic model 
 
 
 
Unsubscribe       Manage 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 sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
 
oxforde_university.jpg
 
 
 
                                 


This email is intended for bionet@evol.mcmaster.ca. ------=_Part_2055333530.1576974155515--