Subject: Bioinformatics Table of Contents for 1 December 2019 ------=_Part_129051587.1576224972502 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Bioinformatics *** Volume 35, Issue 23, 1 December 2019 Read this issue (https://academic.oup.com/bioinformatics/issue/35/23) ------------------------------ Discover high impact research in Bioinformatics Explore our collection of highly cited articles from Bioinformatics. These articles are freely available until the end of 2019. Read now ------------------------------ ============================= DISCOVERY NOTE ============================ Sequence analysis ------------------------------ Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model Chengyu Liu, Yu-Chen Liu, Hsien-Da Huang, Wei Wang (https://academic.oup.com/bioinformatics/article/35/23/4867/5570174) ============================= ORIGINAL PAPERS ============================kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers Peng Jiang, Jie Luo, Yiqi Wang, Pingji Deng, Bertil Schmidt (https://academic.oup.com/bioinformatics/article/35/23/4871/5481953) Efficient multivariate analysis algorithms for longitudinal genome-wide association studies Chao Ning, Dan Wang, Lei Zhou, Julong Wei, Yuanxin Liu (https://academic.oup.com/bioinformatics/article/35/23/4879/5487383) A Bayesian two-way latent structure model for genomic data integration reveals few pan-genomic cluster subtypes in a breast cancer cohort David M Swanson, Tonje Lien, Helga Bergholtz, Therese Sørlie, Arnoldo Frigessi (https://academic.oup.com/bioinformatics/article/35/23/4886/5488120) Prediction of survival risks with adjusted gene expression through risk-gene networks Minhyeok Lee, Sung Won Han, Junhee Seok (https://academic.oup.com/bioinformatics/article/35/23/4898/5490203) Augmented Interval List: a novel data structure for efficient genomic interval search Jianglin Feng, Aakrosh Ratan, Nathan C Sheffield (https://academic.oup.com/bioinformatics/article/35/23/4907/5509521) C-InterSecture---a computational tool for interspecies comparison of genome architecture M Nuriddinov, V Fishman (https://academic.oup.com/bioinformatics/article/35/23/4912/5497251) iRNAD: a computational tool for identifying D modification sites in RNA sequence Zhao-Chun Xu, Peng-Mian Feng, Hui Yang, Wang-Ren Qiu, Wei Chen (https://academic.oup.com/bioinformatics/article/35/23/4922/5488125) Iterative feature representations improve N4-methylcytosine site prediction Leyi Wei, Ran Su, Shasha Luan, Zhijun Liao, Balachandran Manavalan (https://academic.oup.com/bioinformatics/article/35/23/4930/5490856) Benchmarking of 4C-seq pipelines based on real and simulated data Carolin Walter, Daniel Schuetzmann, Frank Rosenbauer, Martin Dugas (https://academic.oup.com/bioinformatics/article/35/23/4938/5499078) ACME: pan-specific peptide--MHC class I binding prediction through attention-based deep neural networks Yan Hu, Ziqiang Wang, Hailin Hu, Fangping Wan, Lin Chen (https://academic.oup.com/bioinformatics/article/35/23/4946/5497763) Joint detection of germline and somatic copy number events in matched tumor--normal sample pairs Yongzhuang Liu, Jian Liu, Yadong Wang (https://academic.oup.com/bioinformatics/article/35/23/4955/5498283) Statistical test of structured continuous trees based on discordance matrix Xiangqi Bai, Liang Ma, Lin Wan (https://academic.oup.com/bioinformatics/article/35/23/4962/5497258) Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery Alvaro Alfayate, Carlos Rodriguez Caceres, Helena Gomes Dos Santos, Ugo Bastolla (https://academic.oup.com/bioinformatics/article/35/23/4971/5481959) FP2VEC: a new molecular featurizer for learning molecular properties Woosung Jeon, Dongsup Kim (https://academic.oup.com/bioinformatics/article/35/23/4979/5487389) CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sergio M Marques (https://academic.oup.com/bioinformatics/article/35/23/4986/5488163) Protein-ensemble--RNA docking by efficient consideration of protein flexibility through homology models Jiahua He, Huanyu Tao, Sheng-You Huang (https://academic.oup.com/bioinformatics/article/35/23/4994/5488970) EROS-DOCK: protein--protein docking using exhaustive branch-and-bound rotational search Maria Elisa Ruiz Echartea, Isaure Chauvot de Beauchêne, David W Ritchie (https://academic.oup.com/bioinformatics/article/35/23/5003/5498285) Exact hypothesis testing for shrinkage-based Gaussian graphical models Victor Bernal, Rainer Bischoff, Victor Guryev, Marco Grzegorczyk, Peter Horvatovich (https://academic.oup.com/bioinformatics/article/35/23/5011/5488126) Accurate differential analysis of transcription factor activity from gene expression Viren Amin, Didem Ağaç, Spencer D Barnes, Murat Can Çobanoğlu (https://academic.oup.com/bioinformatics/article/35/23/5018/5490855) Estimating the strength of expression conservation from high throughput RNA-seq data Xun Gu, Hang Ruan, Jingwen Yang (https://academic.oup.com/bioinformatics/article/35/23/5030/5494699) CoCo: RNA-seq read assignment correction for nested genes and multimapped reads Gabrielle Deschamps-Francoeur, Vincent Boivin, Sherif Abou Elela, Michelle S Scott (https://academic.oup.com/bioinformatics/article/35/23/5039/5505419) PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis Kuan-Ting Lin, Adrian R Krainer (https://academic.oup.com/bioinformatics/article/35/23/5048/5499131) SureTypeSC---a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data Ivan Vogel, Robert C Blanshard, Eva R Hoffmann (https://academic.oup.com/bioinformatics/article/35/23/5055/5497252) Genome analysis ------------------------------ kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers Peng Jiang, Jie Luo, Yiqi Wang, Pingji Deng, Bertil Schmidt (https://academic.oup.com/bioinformatics/article/35/23/4871/5481953) Efficient multivariate analysis algorithms for longitudinal genome-wide association studies Chao Ning, Dan Wang, Lei Zhou, Julong Wei, Yuanxin Liu (https://academic.oup.com/bioinformatics/article/35/23/4879/5487383) A Bayesian two-way latent structure model for genomic data integration reveals few pan-genomic cluster subtypes in a breast cancer cohort David M Swanson, Tonje Lien, Helga Bergholtz, Therese Sørlie, Arnoldo Frigessi (https://academic.oup.com/bioinformatics/article/35/23/4886/5488120) Prediction of survival risks with adjusted gene expression through risk-gene networks Minhyeok Lee, Sung Won Han, Junhee Seok (https://academic.oup.com/bioinformatics/article/35/23/4898/5490203) Augmented Interval List: a novel data structure for efficient genomic interval search Jianglin Feng, Aakrosh Ratan, Nathan C Sheffield (https://academic.oup.com/bioinformatics/article/35/23/4907/5509521) C-InterSecture---a computational tool for interspecies comparison of genome architecture M Nuriddinov, V Fishman (https://academic.oup.com/bioinformatics/article/35/23/4912/5497251) Sequence analysis ------------------------------ iRNAD: a computational tool for identifying D modification sites in RNA sequence Zhao-Chun Xu, Peng-Mian Feng, Hui Yang, Wang-Ren Qiu, Wei Chen (https://academic.oup.com/bioinformatics/article/35/23/4922/5488125) Iterative feature representations improve N4-methylcytosine site prediction Leyi Wei, Ran Su, Shasha Luan, Zhijun Liao, Balachandran Manavalan (https://academic.oup.com/bioinformatics/article/35/23/4930/5490856) Benchmarking of 4C-seq pipelines based on real and simulated data Carolin Walter, Daniel Schuetzmann, Frank Rosenbauer, Martin Dugas (https://academic.oup.com/bioinformatics/article/35/23/4938/5499078) ACME: pan-specific peptide--MHC class I binding prediction through attention-based deep neural networks Yan Hu, Ziqiang Wang, Hailin Hu, Fangping Wan, Lin Chen (https://academic.oup.com/bioinformatics/article/35/23/4946/5497763) Joint detection of germline and somatic copy number events in matched tumor--normal sample pairs Yongzhuang Liu, Jian Liu, Yadong Wang (https://academic.oup.com/bioinformatics/article/35/23/4955/5498283) Phylogenetics ------------------------------ Statistical test of structured continuous trees based on discordance matrix Xiangqi Bai, Liang Ma, Lin Wan (https://academic.oup.com/bioinformatics/article/35/23/4962/5497258) Structural bioinformatics ------------------------------ Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery Alvaro Alfayate, Carlos Rodriguez Caceres, Helena Gomes Dos Santos, Ugo Bastolla (https://academic.oup.com/bioinformatics/article/35/23/4971/5481959) FP2VEC: a new molecular featurizer for learning molecular properties Woosung Jeon, Dongsup Kim (https://academic.oup.com/bioinformatics/article/35/23/4979/5487389) CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sergio M Marques (https://academic.oup.com/bioinformatics/article/35/23/4986/5488163) Protein-ensemble--RNA docking by efficient consideration of protein flexibility through homology models Jiahua He, Huanyu Tao, Sheng-You Huang (https://academic.oup.com/bioinformatics/article/35/23/4994/5488970) EROS-DOCK: protein--protein docking using exhaustive branch-and-bound rotational search Maria Elisa Ruiz Echartea, Isaure Chauvot de Beauchêne, David W Ritchie (https://academic.oup.com/bioinformatics/article/35/23/5003/5498285) Gene expression ------------------------------ Exact hypothesis testing for shrinkage-based Gaussian graphical models Victor Bernal, Rainer Bischoff, Victor Guryev, Marco Grzegorczyk, Peter Horvatovich (https://academic.oup.com/bioinformatics/article/35/23/5011/5488126) Accurate differential analysis of transcription factor activity from gene expression Viren Amin, Didem Ağaç, Spencer D Barnes, Murat Can Çobanoğlu (https://academic.oup.com/bioinformatics/article/35/23/5018/5490855) Estimating the strength of expression conservation from high throughput RNA-seq data Xun Gu, Hang Ruan, Jingwen Yang (https://academic.oup.com/bioinformatics/article/35/23/5030/5494699) CoCo: RNA-seq read assignment correction for nested genes and multimapped reads Gabrielle Deschamps-Francoeur, Vincent Boivin, Sherif Abou Elela, Michelle S Scott (https://academic.oup.com/bioinformatics/article/35/23/5039/5505419) PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis Kuan-Ting Lin, Adrian R Krainer (https://academic.oup.com/bioinformatics/article/35/23/5048/5499131) Genetics and population analysis ------------------------------ SureTypeSC---a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data Ivan Vogel, Robert C Blanshard, Eva R Hoffmann (https://academic.oup.com/bioinformatics/article/35/23/5055/5497252) ============================= APPLICATIONS NOTE ============================ Genome analysis ------------------------------ Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties Lee H Bergstrand, Josh D Neufeld, Andrew C Doxey (https://academic.oup.com/bioinformatics/article/35/23/5063/5522910) 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_129051587.1576224972502 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
Discover high impact research in Bioinformatics
 
Explore our collection of highly cited articles from Bioinformatics. These articles are freely available until the end of 2019.
Read now
 
 
 
 
 
 
Bioinformatics  
Volume 35 Issue 23
 
1 December 2019
 
button-issue.png
 
 
DISCOVERY NOTE
 
 
 
 
Sequence analysis
 
 
 
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model border= 
 
Chengyu Liu ; Yu-Chen Liu; Hsien-Da Huang; Wei Wang
 
 
 
ORIGINAL PAPERS
 
 
 
 
Genome analysis
 
 
 
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers 
 
Peng Jiang; Jie Luo; Yiqi Wang ; Pingji Deng; Bertil Schmidt ...
 
 
Efficient multivariate analysis algorithms for longitudinal genome-wide association studies 
 
Chao Ning; Dan Wang; Lei Zhou ; Julong Wei; Yuanxin Liu ...
 
 
A Bayesian two-way latent structure model for genomic data integration reveals few pan-genomic cluster subtypes in a breast cancer cohort 
 
David M Swanson; Tonje Lien; Helga Bergholtz ; Therese Sørlie; Arnoldo Frigessi
 
 
Prediction of survival risks with adjusted gene expression through risk-gene networks 
 
Minhyeok Lee; Sung Won Han; Junhee Seok
 
 
Augmented Interval List: a novel data structure for efficient genomic interval search 
 
Jianglin Feng; Aakrosh Ratan; Nathan C Sheffield
 
 
C-InterSecture'a computational tool for interspecies comparison of genome architecture 
 
M Nuriddinov; V Fishman
 
 
 
Sequence analysis
 
 
 
iRNAD: a computational tool for identifying D modification sites in RNA sequence 
 
Zhao-Chun Xu; Peng-Mian Feng; Hui Yang ; Wang-Ren Qiu; Wei Chen ...
 
 
Iterative feature representations improve N4-methylcytosine site prediction 
 
Leyi Wei; Ran Su; Shasha Luan ; Zhijun Liao; Balachandran Manavalan ...
 
 
Benchmarking of 4C-seq pipelines based on real and simulated data border= 
 
Carolin Walter ; Daniel Schuetzmann; Frank Rosenbauer; Martin Dugas
 
 
ACME: pan-specific peptide'MHC class I binding prediction through attention-based deep neural networks 
 
Yan Hu; Ziqiang Wang; Hailin Hu ; Fangping Wan; Lin Chen ...
 
 
Joint detection of germline and somatic copy number events in matched tumor'normal sample pairs 
 
Yongzhuang Liu; Jian Liu; Yadong Wang
 
 
 
Phylogenetics
 
 
 
Statistical test of structured continuous trees based on discordance matrix 
 
Xiangqi Bai; Liang Ma; Lin Wan
 
 
 
Structural bioinformatics
 
 
 
Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery 
 
Alvaro Alfayate; Carlos Rodriguez Caceres; Helena Gomes Dos Santos ; Ugo Bastolla
 
 
FP2VEC: a new molecular featurizer for learning molecular properties 
 
Woosung Jeon; Dongsup Kim
 
 
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels 
 
Ondrej Vavra; Jiri Filipovic; Jan Plhak ; David Bednar; Sergio M Marques ...
 
 
Protein-ensemble'RNA docking by efficient consideration of protein flexibility through homology models 
 
Jiahua He; Huanyu Tao; Sheng-You Huang
 
 
EROS-DOCK: protein'protein docking using exhaustive branch-and-bound rotational search 
 
Maria Elisa Ruiz Echartea; Isaure Chauvot de Beauchêne; David W Ritchie
 
 
 
Gene expression
 
 
 
Exact hypothesis testing for shrinkage-based Gaussian graphical models border= 
 
Victor Bernal ; Rainer Bischoff; Victor Guryev; Marco Grzegorczyk; Peter Horvatovich
 
 
Accurate differential analysis of transcription factor activity from gene expression 
 
Viren Amin; Didem Ağaç; Spencer D Barnes ; Murat Can Çobanoğlu
 
 
Estimating the strength of expression conservation from high throughput RNA-seq data 
 
Xun Gu; Hang Ruan; Jingwen Yang
 
 
CoCo: RNA-seq read assignment correction for nested genes and multimapped reads border= 
 
Gabrielle Deschamps-Francoeur ; Vincent Boivin; Sherif Abou Elela; Michelle S Scott
 
 
PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis 
 
Kuan-Ting Lin; Adrian R Krainer
 
 
 
Genetics and population analysis
 
 
 
SureTypeSC'a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data 
 
Ivan Vogel; Robert C Blanshard; Eva R Hoffmann
 
 
 
APPLICATIONS NOTE
 
 
 
 
Genome analysis
 
 
 
Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties 
 
Lee H Bergstrand; Josh D Neufeld; Andrew C Doxey
 
 
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