Subject: Bioinformatics Table of Contents for 15 January 2020 ------=_Part_1391887619.1580232132238 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Bioinformatics *** Volume 36, Issue 2, 15 January 2020 Read this issue (https://academic.oup.com/bioinformatics/issue/36/2) ------------------------------ 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 ------------------------------ ============================= ORIGINAL PAPERS ============================Bayesian estimation of genetic regulatory effects in high-throughput reporter assays William H Majoros, Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang (https://academic.oup.com/bioinformatics/article/36/2/331/5542384) Identification of expression signatures for non-small-cell lung carcinoma subtype classification Ran Su, Jiahang Zhang, Xiaofeng Liu, Leyi Wei (https://academic.oup.com/bioinformatics/article/36/2/339/5531132) Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data Chan Wang, Jiyuan Hu, Martin J Blaser, Huilin Li (https://academic.oup.com/bioinformatics/article/36/2/347/5536874) MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies Terry Ma, Di Xiao, Xin Xing (https://academic.oup.com/bioinformatics/article/36/2/356/5538989) Predicting the effects of SNPs on transcription factor binding affinity Sierra S Nishizaki, Natalie Ng, Shengcheng Dong, Robert S Porter, Cody Morterud (https://academic.oup.com/bioinformatics/article/36/2/364/5543098) ArtiFuse'computational validation of fusion gene detection tools without relying on simulated reads Patrick Sorn, Christoph Holtsträter, Martin Löwer, Ugur Sahin, David Weber (https://academic.oup.com/bioinformatics/article/36/2/373/5543101) Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models Alfredo Velasco, II, Benjamin T James, Vincent D Wells, Hani Z Girgis (https://academic.oup.com/bioinformatics/article/36/2/380/5530162) MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model Cong Pian, Guangle Zhang, Fei Li, Xiaodan Fan (https://academic.oup.com/bioinformatics/article/36/2/388/5531135) QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable Michele Berselli, Enrico Lavezzo, Stefano Toppo (https://academic.oup.com/bioinformatics/article/36/2/393/5536767) Haplotype-aware graph indexes Jouni Sirén, Erik Garrison, Adam M Novak, Benedict Paten, Richard Durbin (https://academic.oup.com/bioinformatics/article/36/2/400/5538990) How sequence alignment scores correspond to probability models Martin C Frith (https://academic.oup.com/bioinformatics/article/36/2/408/5536873) THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage Chloé Dimeglio, Stéphanie Raymond, Nicolas Jeanne, Christelle Reynes, Romain Carcenac (https://academic.oup.com/bioinformatics/article/36/2/416/5539688) DeepGOPlus: improved protein function prediction from sequence Maxat Kulmanov, Robert Hoehndorf (https://academic.oup.com/bioinformatics/article/36/2/422/5539866) The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation Roberto Del Amparo, Alberto Vicens, Miguel Arenas (https://academic.oup.com/bioinformatics/article/36/2/430/5532222) Artificial intelligence-based multi-objective optimization protocol for protein structure refinement Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang (https://academic.oup.com/bioinformatics/article/36/2/437/5528501) DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing Justin Chan, Jinhao Zou, Christopher Llynard Ortiz, Chi-Hong Chang Chien, Rong-Long Pan (https://academic.oup.com/bioinformatics/article/36/2/449/5538986) pourRNA'a time- and memory-efficient approach for the guided exploration of RNA energy landscapes Gregor Entzian, Martin Raden (https://academic.oup.com/bioinformatics/article/36/2/462/5539864) DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout Badri Adhikari (https://academic.oup.com/bioinformatics/article/36/2/470/5540673) Topology-independent and global protein structure alignment through an FFT-based algorithm Zeyu Wen, Jiahua He, Sheng-You Huang (https://academic.oup.com/bioinformatics/article/36/2/478/5544106) GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis Adib Shafi, Tin Nguyen, Azam Peyvandipour, Sorin Draghici (https://academic.oup.com/bioinformatics/article/36/2/487/5536878) Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network Wanwen Zeng, Yong Wang, Rui Jiang (https://academic.oup.com/bioinformatics/article/36/2/496/5535598) ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses Christelle Reynès, Guilhem Kister, Marine Rohmer, Tristan Bouschet, Annie Varrault (https://academic.oup.com/bioinformatics/article/36/2/504/5539691) MOOMIN ' Mathematical explOration of 'Omics data on a MetabolIc Network Taneli Pusa, Mariana Galvao Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela (https://academic.oup.com/bioinformatics/article/36/2/514/5553096) P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications Zhiguang Huo, Shaowu Tang, Yongseok Park, George Tseng (https://academic.oup.com/bioinformatics/article/36/2/524/5540321) ACTINN: automated identification of cell types in single cell RNA sequencing Feiyang Ma, Matteo Pellegrini (https://academic.oup.com/bioinformatics/article/36/2/533/5540320) circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs Li Chen, Feng Wang, Emily C Bruggeman, Chao Li, Bing Yao (https://academic.oup.com/bioinformatics/article/36/2/539/5543088) VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data Kyungsoo Kim, Sunmo Yang, Sang-Jun Ha, Insuk Lee (https://academic.oup.com/bioinformatics/article/36/2/546/5543087) Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease Lerato E Magosi, on behalf of the CARDIoGRAMplusC4D Consortium, Anuj Goel, on behalf of the CARDIoGRAMplusC4D Consortium, Jemma C Hopewell (https://academic.oup.com/bioinformatics/article/36/2/552/5539865) Comparison of single and module-based methods for modeling gene regulatory networks Mikel Hernaez, Charles Blatti, Olivier Gevaert (https://academic.oup.com/bioinformatics/article/36/2/558/5530163) Identifying emerging phenomenon in long temporal phenotyping experiments Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S Dina, Xuequn Shang (https://academic.oup.com/bioinformatics/article/36/2/568/5532221) ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics Ning Shi, Zexuan Zhu, Ke Tang, David Parker, Shan He (https://academic.oup.com/bioinformatics/article/36/2/578/5542393) Bayesian inference of distributed time delay in transcriptional and translational regulation Boseung Choi, Yu-Yu Cheng, Selahattin Cinar, William Ott, Matthew R Bennett (https://academic.oup.com/bioinformatics/article/36/2/586/5538987) Efficient parameterization of large-scale dynamic models based on relative measurements Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl (https://academic.oup.com/bioinformatics/article/36/2/594/5538985) Discovering protein drug targets using knowledge graph embeddings Sameh K Mohamed, Vít Nováček, Aayah Nounu (https://academic.oup.com/bioinformatics/article/36/2/603/5542390) BioNorm: deep learning-based event normalization for the curation of reaction databases Peiliang Lou, Antonio Jimeno Yepes, Zai Zhang, Qinghua Zheng, Xiangrong Zhang (https://academic.oup.com/bioinformatics/article/36/2/611/5539693) Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping Siva Rajesh Kasa, Sakyajit Bhattacharya, Vaibhav Rajan (https://academic.oup.com/bioinformatics/article/36/2/621/5542387) Non-parametric individual treatment effect estimation for survival data with random forests Sami Tabib, Denis Larocque (https://academic.oup.com/bioinformatics/article/36/2/629/5542949) Context awareness and embedding for biomedical event extraction Shankai Yan, Ka-Chun Wong (https://academic.oup.com/bioinformatics/article/36/2/637/5544930) GENOME ANALYSIS ------------------------------ Bayesian estimation of genetic regulatory effects in high-throughput reporter assays William H Majoros, Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang (https://academic.oup.com/bioinformatics/article/36/2/331/5542384) Identification of expression signatures for non-small-cell lung carcinoma subtype classification Ran Su, Jiahang Zhang, Xiaofeng Liu, Leyi Wei (https://academic.oup.com/bioinformatics/article/36/2/339/5531132) Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data Chan Wang, Jiyuan Hu, Martin J Blaser, Huilin Li (https://academic.oup.com/bioinformatics/article/36/2/347/5536874) MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies Terry Ma, Di Xiao, Xin Xing (https://academic.oup.com/bioinformatics/article/36/2/356/5538989) Predicting the effects of SNPs on transcription factor binding affinity Sierra S Nishizaki, Natalie Ng, Shengcheng Dong, Robert S Porter, Cody Morterud (https://academic.oup.com/bioinformatics/article/36/2/364/5543098) ArtiFuse'computational validation of fusion gene detection tools without relying on simulated reads Patrick Sorn, Christoph Holtsträter, Martin Löwer, Ugur Sahin, David Weber (https://academic.oup.com/bioinformatics/article/36/2/373/5543101) SEQUENCE ANALYSIS ------------------------------ Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models Alfredo Velasco, II, Benjamin T James, Vincent D Wells, Hani Z Girgis (https://academic.oup.com/bioinformatics/article/36/2/380/5530162) MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model Cong Pian, Guangle Zhang, Fei Li, Xiaodan Fan (https://academic.oup.com/bioinformatics/article/36/2/388/5531135) QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable Michele Berselli, Enrico Lavezzo, Stefano Toppo (https://academic.oup.com/bioinformatics/article/36/2/393/5536767) Haplotype-aware graph indexes Jouni Sirén, Erik Garrison, Adam M Novak, Benedict Paten, Richard Durbin (https://academic.oup.com/bioinformatics/article/36/2/400/5538990) How sequence alignment scores correspond to probability models Martin C Frith (https://academic.oup.com/bioinformatics/article/36/2/408/5536873) THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage Chloé Dimeglio, Stéphanie Raymond, Nicolas Jeanne, Christelle Reynes, Romain Carcenac (https://academic.oup.com/bioinformatics/article/36/2/416/5539688) DeepGOPlus: improved protein function prediction from sequence Maxat Kulmanov, Robert Hoehndorf (https://academic.oup.com/bioinformatics/article/36/2/422/5539866) PHYLOGENETICS ------------------------------ The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation Roberto Del Amparo, Alberto Vicens, Miguel Arenas (https://academic.oup.com/bioinformatics/article/36/2/430/5532222) STRUCTURAL BIOINFORMATICS ------------------------------ Artificial intelligence-based multi-objective optimization protocol for protein structure refinement Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang (https://academic.oup.com/bioinformatics/article/36/2/437/5528501) DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing Justin Chan, Jinhao Zou, Christopher Llynard Ortiz, Chi-Hong Chang Chien, Rong-Long Pan (https://academic.oup.com/bioinformatics/article/36/2/449/5538986) pourRNA'a time- and memory-efficient approach for the guided exploration of RNA energy landscapes Gregor Entzian, Martin Raden (https://academic.oup.com/bioinformatics/article/36/2/462/5539864) DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout Badri Adhikari (https://academic.oup.com/bioinformatics/article/36/2/470/5540673) Topology-independent and global protein structure alignment through an FFT-based algorithm Zeyu Wen, Jiahua He, Sheng-You Huang (https://academic.oup.com/bioinformatics/article/36/2/478/5544106) GENE EXPRESSION ------------------------------ GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis Adib Shafi, Tin Nguyen, Azam Peyvandipour, Sorin Draghici (https://academic.oup.com/bioinformatics/article/36/2/487/5536878) Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network Wanwen Zeng, Yong Wang, Rui Jiang (https://academic.oup.com/bioinformatics/article/36/2/496/5535598) ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses Christelle Reynès, Guilhem Kister, Marine Rohmer, Tristan Bouschet, Annie Varrault (https://academic.oup.com/bioinformatics/article/36/2/504/5539691) MOOMIN ' Mathematical explOration of 'Omics data on a MetabolIc Network Taneli Pusa, Mariana Galvao Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela (https://academic.oup.com/bioinformatics/article/36/2/514/5553096) P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications Zhiguang Huo, Shaowu Tang, Yongseok Park, George Tseng (https://academic.oup.com/bioinformatics/article/36/2/524/5540321) ACTINN: automated identification of cell types in single cell RNA sequencing Feiyang Ma, Matteo Pellegrini (https://academic.oup.com/bioinformatics/article/36/2/533/5540320) circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs Li Chen, Feng Wang, Emily C Bruggeman, Chao Li, Bing Yao (https://academic.oup.com/bioinformatics/article/36/2/539/5543088) VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data Kyungsoo Kim, Sunmo Yang, Sang-Jun Ha, Insuk Lee (https://academic.oup.com/bioinformatics/article/36/2/546/5543087) GENETICS AND POPULATION ANALYSIS ------------------------------ Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease Lerato E Magosi, on behalf of the CARDIoGRAMplusC4D Consortium, Anuj Goel, on behalf of the CARDIoGRAMplusC4D Consortium, Jemma C Hopewell (https://academic.oup.com/bioinformatics/article/36/2/552/5539865) SYSTEMS BIOLOGY ------------------------------ Comparison of single and module-based methods for modeling gene regulatory networks Mikel Hernaez, Charles Blatti, Olivier Gevaert (https://academic.oup.com/bioinformatics/article/36/2/558/5530163) Identifying emerging phenomenon in long temporal phenotyping experiments Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S Dina, Xuequn Shang (https://academic.oup.com/bioinformatics/article/36/2/568/5532221) ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics Ning Shi, Zexuan Zhu, Ke Tang, David Parker, Shan He (https://academic.oup.com/bioinformatics/article/36/2/578/5542393) Bayesian inference of distributed time delay in transcriptional and translational regulation Boseung Choi, Yu-Yu Cheng, Selahattin Cinar, William Ott, Matthew R Bennett (https://academic.oup.com/bioinformatics/article/36/2/586/5538987) Efficient parameterization of large-scale dynamic models based on relative measurements Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl (https://academic.oup.com/bioinformatics/article/36/2/594/5538985) Discovering protein drug targets using knowledge graph embeddings Sameh K Mohamed, Vít Nováček, Aayah Nounu (https://academic.oup.com/bioinformatics/article/36/2/603/5542390) DATA AND TEXT MINING ------------------------------ BioNorm: deep learning-based event normalization for the curation of reaction databases Peiliang Lou, Antonio Jimeno Yepes, Zai Zhang, Qinghua Zheng, Xiangrong Zhang (https://academic.oup.com/bioinformatics/article/36/2/611/5539693) Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping Siva Rajesh Kasa, Sakyajit Bhattacharya, Vaibhav Rajan (https://academic.oup.com/bioinformatics/article/36/2/621/5542387) Non-parametric individual treatment effect estimation for survival data with random forests Sami Tabib, Denis Larocque (https://academic.oup.com/bioinformatics/article/36/2/629/5542949) Context awareness and embedding for biomedical event extraction Shankai Yan, Ka-Chun Wong (https://academic.oup.com/bioinformatics/article/36/2/637/5544930) ============================= APPLICATIONS NOTES ============================DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data R N Ramirez, K Bedirian, S M Gray, A Diallo (https://academic.oup.com/bioinformatics/article/36/2/644/5543099) RAG-Web: RNA structure prediction/design using RNA-As-Graphs Grace Meng, Marva Tariq, Swati Jain, Shereef Elmetwaly, Tamar Schlick (https://academic.oup.com/bioinformatics/article/36/2/647/5543100) gwasrapidd: an R package to query, download and wrangle GWAS catalog data Ramiro Magno, Ana-Teresa Maia (https://academic.oup.com/bioinformatics/article/36/2/649/5543089) GENOME ANALYSIS ------------------------------ DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data R N Ramirez, K Bedirian, S M Gray, A Diallo (https://academic.oup.com/bioinformatics/article/36/2/644/5543099) STRUCTURAL BIOINFORMATICS ------------------------------ RAG-Web: RNA structure prediction/design using RNA-As-Graphs Grace Meng, Marva Tariq, Swati Jain, Shereef Elmetwaly, Tamar Schlick (https://academic.oup.com/bioinformatics/article/36/2/647/5543100) DATA AND TEXT MINING ------------------------------ gwasrapidd: an R package to query, download and wrangle GWAS catalog data Ramiro Magno, Ana-Teresa Maia (https://academic.oup.com/bioinformatics/article/36/2/649/5543089) ============================= CORRIGENDUM ============================Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs Antoine Limasset, Jean-François Flot, Pierre Peterlongo (https://academic.oup.com/bioinformatics/article/36/2/651/5662392) 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_1391887619.1580232132238 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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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 36 Issue 2
 
15 January 2020
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Bayesian estimation of genetic regulatory effects in high-throughput reporter assays 
 
William H Majoros; Young-Sook Kim; Alejandro Barrera ; Fan Li; Xingyan Wang ...
 
 
Identification of expression signatures for non-small-cell lung carcinoma subtype classification 
 
Ran Su; Jiahang Zhang; Xiaofeng Liu ; Leyi Wei
 
 
Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data 
 
Chan Wang; Jiyuan Hu; Martin J Blaser ; Huilin Li
 
 
MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies 
 
Terry Ma; Di Xiao; Xin Xing
 
 
Predicting the effects of SNPs on transcription factor binding affinity 
 
Sierra S Nishizaki; Natalie Ng; Shengcheng Dong ; Robert S Porter; Cody Morterud ...
 
 
ArtiFuse'computational validation of fusion gene detection tools without relying on simulated reads 
 
Patrick Sorn; Christoph Holtsträter; Martin Löwer ; Ugur Sahin; David Weber
 
 
 
SEQUENCE ANALYSIS
 
 
 
Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models 
 
Alfredo Velasco, II; Benjamin T James; Vincent D Wells ; Hani Z Girgis
 
 
MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model 
 
Cong Pian; Guangle Zhang; Fei Li ; Xiaodan Fan
 
 
QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable 
 
Michele Berselli; Enrico Lavezzo; Stefano Toppo
 
 
Haplotype-aware graph indexes border=  
 
Jouni Sirén; Erik Garrison; Adam M Novak ; Benedict Paten; Richard Durbin
 
 
How sequence alignment scores correspond to probability models border= 
 
Martin C Frith
 
 
THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage 
 
Chloé Dimeglio; Stéphanie Raymond; Nicolas Jeanne ; Christelle Reynes; Romain Carcenac ...
 
 
DeepGOPlus: improved protein function prediction from sequence border= 
 
Maxat Kulmanov ; Robert Hoehndorf
 
 
 
PHYLOGENETICS
 
 
 
The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation 
 
Roberto Del Amparo; Alberto Vicens; Miguel Arenas
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement 
 
Di Wang; Ling Geng; Yu-Jun Zhao ; Yang Yang; Yan Huang ...
 
 
DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing 
 
Justin Chan; Jinhao Zou; Christopher Llynard Ortiz ; Chi-Hong Chang Chien; Rong-Long Pan ...
 
 
pourRNA'a time- and memory-efficient approach for the guided exploration of RNA energy landscapes 
 
Gregor Entzian; Martin Raden
 
 
DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout 
 
Badri Adhikari
 
 
Topology-independent and global protein structure alignment through an FFT-based algorithm 
 
Zeyu Wen; Jiahua He; Sheng-You Huang
 
 
 
GENE EXPRESSION
 
 
 
GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis 
 
Adib Shafi; Tin Nguyen; Azam Peyvandipour ; Sorin Draghici
 
 
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network 
 
Wanwen Zeng; Yong Wang; Rui Jiang
 
 
ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses border= 
 
Christelle Reynès ; Guilhem Kister; Marine Rohmer; Tristan Bouschet; Annie Varrault ...
 
 
MOOMIN ' Mathematical explOration of 'Omics data on a MetabolIc Network border= 
 
Taneli Pusa ; Mariana Galvão Ferrarini; Ricardo Andrade; Arnaud Mary; Alberto Marchetti-Spaccamela ...
 
 
P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications 
 
Zhiguang Huo; Shaowu Tang; Yongseok Park ; George Tseng
 
 
ACTINN: automated identification of cell types in single cell RNA sequencing 
 
Feiyang Ma; Matteo Pellegrini
 
 
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs 
 
Li Chen; Feng Wang; Emily C Bruggeman ; Chao Li; Bing Yao
 
 
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data border= 
 
Kyungsoo Kim ; Sunmo Yang; Sang-Jun Ha; Insuk Lee
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease border= 
 
Lerato E Magosi ; on behalf of the CARDIoGRAMplusC4D Consortium; Anuj Goel; on behalf of the CARDIoGRAMplusC4D Consortium; Jemma C Hopewell ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Comparison of single and module-based methods for modeling gene regulatory networks 
 
Mikel Hernaez; Charles Blatti; Olivier Gevaert
 
 
Identifying emerging phenomenon in long temporal phenotyping experiments 
 
Jiajie Peng; Junya Lu; Donghee Hoh ; Ayesha S Dina; Xuequn Shang ...
 
 
ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics 
 
Ning Shi; Zexuan Zhu; Ke Tang ; David Parker; Shan He
 
 
Bayesian inference of distributed time delay in transcriptional and translational regulation 
 
Boseung Choi; Yu-Yu Cheng; Selahattin Cinar ; William Ott; Matthew R Bennett ...
 
 
Efficient parameterization of large-scale dynamic models based on relative measurements border= 
 
Leonard Schmiester ; Yannik Schälte; Fabian Fröhlich; Jan Hasenauer; Daniel Weindl
 
 
Discovering protein drug targets using knowledge graph embeddings 
 
Sameh K Mohamed; Vít Nováček; Aayah Nounu
 
 
 
DATA AND TEXT MINING
 
 
 
BioNorm: deep learning-based event normalization for the curation of reaction databases 
 
Peiliang Lou; Antonio Jimeno Yepes; Zai Zhang ; Qinghua Zheng; Xiangrong Zhang ...
 
 
Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping 
 
Siva Rajesh Kasa; Sakyajit Bhattacharya; Vaibhav Rajan
 
 
Non-parametric individual treatment effect estimation for survival data with random forests 
 
Sami Tabib; Denis Larocque
 
 
Context awareness and embedding for biomedical event extraction 
 
Shankai Yan; Ka-Chun Wong
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data 
 
R N Ramirez; K Bedirian; S M Gray ; A Diallo
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
RAG-Web: RNA structure prediction/design using RNA-As-Graphs 
 
Grace Meng; Marva Tariq; Swati Jain ; Shereef Elmetwaly; Tamar Schlick
 
 
 
DATA AND TEXT MINING
 
 
 
gwasrapidd: an R package to query, download and wrangle GWAS catalog data border= 
 
Ramiro Magno ; Ana-Teresa Maia
 
 
 
CORRIGENDUM
 
 
 
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs 
 
Antoine Limasset; Jean-François Flot; Pierre Peterlongo
 
 
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