Subject: Briefings in Bioinformatics Table of Contents for July 2019 ------=_Part_179473036.1570816692129 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** {Briefings in Bioinformatics} *** Volume 20, Issue 4, 19 July 2019 Read this issue (https://academic.oup.com/bib/issue/20/4) ------------------------------ 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 ------------------------------ ============================= Paper ============================Microbial genome analysis: the COG approach Michael Y Galperin, David M Kristensen, Kira S Makarova, Yuri I Wolf, Eugene V Koonin (https://academic.oup.com/bib/article/20/4/1063/4158183) MicroScope---an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Guillaume Gautreau (https://academic.oup.com/bib/article/20/4/1071/4157326) The BioCyc collection of microbial genomes and metabolic pathways Peter D Karp, Richard Billington, Ron Caspi, Carol A Fulcher, Mario Latendresse (https://academic.oup.com/bib/article/20/4/1085/4084231) PATRIC as a unique resource for studying antimicrobial resistance Dionysios A Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas Brettin, Christopher Bun (https://academic.oup.com/bib/article/20/4/1094/4056412) Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters Kai Blin, Hyun Uk Kim, Marnix H Medema, Tilmann Weber (https://academic.oup.com/bib/article/20/4/1103/4590131) Recent development of Ori-Finder system and DoriC database for microbial replication origins Hao Luo, Chun-Lan Quan, Chong Peng, Feng Gao (https://academic.oup.com/bib/article/20/4/1114/4796864) A review of methods and databases for metagenomic classification and assembly Florian P Breitwieser, Jennifer Lu, Steven L Salzberg (https://academic.oup.com/bib/article/20/4/1125/4210288) Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes Nathan D Olson, Todd J Treangen, Christopher M Hill, Victoria Cepeda-Espinoza, Jay Ghurye (https://academic.oup.com/bib/article/20/4/1140/4075034) MG-RAST version 4---lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis Folker Meyer, Saurabh Bagchi, Somali Chaterji, Wolfgang Gerlach, Ananth Grama (https://academic.oup.com/bib/article/20/4/1151/4237462) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization Kazutaka Katoh, John Rozewicki, Kazunori D Yamada (https://academic.oup.com/bib/article/20/4/1160/4106928) Towards dynamic genome-scale models David Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr (https://academic.oup.com/bib/article/20/4/1167/4524047) Computational tools for plant small RNA detection and categorization Lionel Morgado, Frank Johannes (https://academic.oup.com/bib/article/20/4/1181/4558649) Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk Yongsheng Li, Xiyun Jin, Zishan Wang, Lili Li, Hong Chen (https://academic.oup.com/bib/article/20/4/1193/4565515) Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures Jincheol Park, Shili Lin (https://academic.oup.com/bib/article/20/4/1205/4582342) A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects Gerhard Mayer, Christian Quast, Janine Felden, Matthias Lange, Manuel Prinz (https://academic.oup.com/bib/article/20/4/1215/4582343) A survey and evaluations of histogram-based statistics in alignment-free sequence comparison Brian B Luczak, Benjamin T James, Hani Z Girgis (https://academic.oup.com/bib/article/20/4/1222/4696316) Conceptual and computational framework for logical modelling of biological networks deregulated in diseases Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot (https://academic.oup.com/bib/article/20/4/1238/4716963) Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains Jian Zhang, Zhiqiang Ma, Lukasz Kurgan (https://academic.oup.com/bib/article/20/4/1250/4748786) Multi-omics integration---a comparison of unsupervised clustering methodologies Giulia Tini, Luca Marchetti, Corrado Priami, Marie-Pier Scott-Boyer (https://academic.oup.com/bib/article/20/4/1269/4758623) BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches Bin Liu (https://academic.oup.com/bib/article/20/4/1280/4763667) Link synthetic lethality to drug sensitivity of cancer cells Ruiping Wang, Yue Han, Zhangxiang Zhao, Fan Yang, Tingting Chen (https://academic.oup.com/bib/article/20/4/1295/4781362) Drug knowledge bases and their applications in biomedical informatics research Yongjun Zhu, Olivier Elemento, Jyotishman Pathak, Fei Wang (https://academic.oup.com/bib/article/20/4/1308/4785946) SEGreg: a database for human specifically expressed genes and their regulations in cancer and normal tissue Qin Tang, Qiong Zhang, Yao Lv, Ya-Ru Miao, An-Yuan Guo (https://academic.oup.com/bib/article/20/4/1322/4786617) Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology Florencio Pazos, Monica Chagoyen (https://academic.oup.com/bib/article/20/4/1329/4812639) Computational prediction of drug--target interactions using chemogenomic approaches: an empirical survey Ali Ezzat, Min Wu, Xiao-Li Li, Chee-Keong Kwoh (https://academic.oup.com/bib/article/20/4/1337/4824712) Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors Fernando Carazo, Juan P Romero, Angel Rubio (https://academic.oup.com/bib/article/20/4/1358/4829658) Modeling biological problems in computer science: a case study in genome assembly Paul Medvedev (https://academic.oup.com/bib/article/20/4/1376/4830907) How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives Alessandra Dal Molin, Barbara Di Camillo (https://academic.oup.com/bib/article/20/4/1384/4831233) Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems Andrés Zalguizuri, Gustavo Caetano-Anollés, Viviana Claudia Lepek (https://academic.oup.com/bib/article/20/4/1395/4831237) Inferring and analyzing module-specific lncRNA--mRNA causal regulatory networks in human cancer Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li (https://academic.oup.com/bib/article/20/4/1403/4833470) Microarray is an efficient tool for circRNA profiling Shasha Li, Shuaishuai Teng, Junquan Xu, Guannan Su, Yu Zhang (https://academic.oup.com/bib/article/20/4/1420/4837254) Artificial intelligence in drug combination therapy Igor F Tsigelny (https://academic.oup.com/bib/article/20/4/1434/4846893) It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao (https://academic.oup.com/bib/article/20/4/1449/4911545) Open-source chemogenomic data-driven algorithms for predicting drug--target interactions Ming Hao, Stephen H Bryant, Yanli Wang (https://academic.oup.com/bib/article/20/4/1465/4840612) ============================= Review Article ============================Where to search top-K biomedical ontologies? Daniela Oliveira, Anila Sahar Butt, Armin Haller, Dietrich Rebholz-Schuhmann, Ratnesh Sahay (https://academic.oup.com/bib/article/20/4/1477/4944514) Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network Jue Yang, Hui Song, Kun Cao, Jialei Song, Jianjiang Zhou (https://academic.oup.com/bib/article/20/4/1492/4944515) Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor Hua Sun, Pora Kim, Peilin Jia, Ae Kyung Park, Han Liang (https://academic.oup.com/bib/article/20/4/1502/4944720) Interactive and coordinated visualization approaches for biological data analysis António Cruz, Joel P Arrais, Penousal Machado (https://academic.oup.com/bib/article/20/4/1513/4953976) A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data Zhuo Zhang, Hao Li, Shuai Jiang, Ruijiang Li, Wanying Li (https://academic.oup.com/bib/article/20/4/1524/4956394) Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions Damla Senol Cali, Jeremie S Kim, Saugata Ghose, Can Alkan, Onur Mutlu (https://academic.oup.com/bib/article/20/4/1542/4958758) ============================= Software Review ============================PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes David Arndt, Ana Marcu, Yongjie Liang, David S Wishart (https://academic.oup.com/bib/article/20/4/1560/4222653) DOOR: a prokaryotic operon database for genome analyses and functional inference Huansheng Cao, Qin Ma, Xin Chen, Ying Xu (https://academic.oup.com/bib/article/20/4/1568/4055922) Visualizing and comparing circular genomes using the CGView family of tools Paul Stothard, Jason R Grant, Gary Van Domselaar (https://academic.oup.com/bib/article/20/4/1576/4037458) Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data Shun H Yip, Pak Chung Sham, Junwen Wang (https://academic.oup.com/bib/article/20/4/1583/4898116) ============================= Case Study ============================Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes Gaoyang Li, Huansheng Cao, Ying Xu (https://academic.oup.com/bib/article/20/4/1590/4955282) 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_179473036.1570816692129 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 4
 
July 2019
 
button-issue.png
 
 
Paper
 
 
 
Microbial genome analysis: the COG approach 
 
Michael Y Galperin; David M Kristensen; Kira S Makarova ; Yuri I Wolf; Eugene V Koonin
 
 
MicroScope'an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data border= 
 
Claudine Médigue ; Alexandra Calteau; Stéphane Cruveiller; Mathieu Gachet; Guillaume Gautreau ...
 
 
The BioCyc collection of microbial genomes and metabolic pathways 
 
Peter D Karp; Richard Billington; Ron Caspi ; Carol A Fulcher; Mario Latendresse ...
 
 
PATRIC as a unique resource for studying antimicrobial resistance border= 
 
Dionysios A Antonopoulos ; Rida Assaf; Ramy Karam Aziz; Thomas Brettin; Christopher Bun ...
 
 
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters border= 
 
Kai Blin ; Hyun Uk Kim; Marnix H Medema; Tilmann Weber
 
 
Recent development of Ori-Finder system and DoriC database for microbial replication origins 
 
Hao Luo; Chun-Lan Quan; Chong Peng ; Feng Gao
 
 
A review of methods and databases for metagenomic classification and assembly 
 
Florian P Breitwieser; Jennifer Lu; Steven L Salzberg
 
 
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes 
 
Nathan D Olson; Todd J Treangen; Christopher M Hill ; Victoria Cepeda-Espinoza; Jay Ghurye ...
 
 
MG-RAST version 4'lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis 
 
Folker Meyer; Saurabh Bagchi; Somali Chaterji ; Wolfgang Gerlach; Ananth Grama ...
 
 
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization border= 
 
Kazutaka Katoh ; John Rozewicki; Kazunori D Yamada
 
 
Towards dynamic genome-scale models border=  
 
David Gilbert; Monika Heiner; Yasoda Jayaweera; Christian Rohr
 
 
Computational tools for plant small RNA detection and categorization border= 
 
Lionel Morgado ; Frank Johannes
 
 
Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk 
 
Yongsheng Li; Xiyun Jin; Zishan Wang ; Lili Li; Hong Chen ...
 
 
Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures 
 
Jincheol Park; Shili Lin
 
 
A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects border= 
 
Gerhard Mayer ; Christian Quast; Janine Felden; Matthias Lange; Manuel Prinz ...
 
 
A survey and evaluations of histogram-based statistics in alignment-free sequence comparison border= 
 
Brian B Luczak ; Benjamin T James; Hani Z Girgis
 
 
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases 
 
Arnau Montagud; Pauline Traynard; Loredana Martignetti ; Eric Bonnet; Emmanuel Barillot ...
 
 
Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains 
 
Jian Zhang; Zhiqiang Ma; Lukasz Kurgan
 
 
Multi-omics integration'a comparison of unsupervised clustering methodologies 
 
Giulia Tini; Luca Marchetti; Corrado Priami ; Marie-Pier Scott-Boyer
 
 
BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches 
 
Bin Liu
 
 
Link synthetic lethality to drug sensitivity of cancer cells 
 
Ruiping Wang; Yue Han; Zhangxiang Zhao ; Fan Yang; Tingting Chen ...
 
 
Drug knowledge bases and their applications in biomedical informatics research 
 
Yongjun Zhu; Olivier Elemento; Jyotishman Pathak ; Fei Wang
 
 
SEGreg: a database for human specifically expressed genes and their regulations in cancer and normal tissue 
 
Qin Tang; Qiong Zhang; Yao Lv ; Ya-Ru Miao; An-Yuan Guo
 
 
Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology 
 
Florencio Pazos; Monica Chagoyen
 
 
Computational prediction of drug'target interactions using chemogenomic approaches: an empirical survey 
 
Ali Ezzat; Min Wu; Xiao-Li Li ; Chee-Keong Kwoh
 
 
Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors 
 
Fernando Carazo; Juan P Romero; Angel Rubio
 
 
Modeling biological problems in computer science: a case study in genome assembly 
 
Paul Medvedev
 
 
How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives 
 
Alessandra Dal Molin; Barbara Di Camillo
 
 
Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems  
 
Andrés Zalguizuri; Gustavo Caetano-Anollés ; Viviana Claudia Lepek
 
 
Inferring and analyzing module-specific lncRNA'mRNA causal regulatory networks in human cancer 
 
Junpeng Zhang; Thuc Duy Le; Lin Liu ; Jiuyong Li
 
 
Microarray is an efficient tool for circRNA profiling 
 
Shasha Li; Shuaishuai Teng; Junquan Xu ; Guannan Su; Yu Zhang ...
 
 
Artificial intelligence in drug combination therapy 
 
Igor F Tsigelny
 
 
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data 
 
Juan Xie; Anjun Ma; Anne Fennell ; Qin Ma; Jing Zhao
 
 
Open-source chemogenomic data-driven algorithms for predicting drug'target interactions 
 
Ming Hao; Stephen H Bryant; Yanli Wang
 
 
 
Review Article
 
 
 
Where to search top-K biomedical ontologies? border= 
 
Daniela Oliveira; Anila Sahar Butt; Armin Haller; Dietrich Rebholz-Schuhmann; Ratnesh Sahay
 
 
Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network border= 
 
Jue Yang ; Hui Song; Kun Cao; Jialei Song; Jianjiang Zhou
 
 
Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor 
 
Hua Sun; Pora Kim; Peilin Jia ; Ae Kyung Park; Han Liang ...
 
 
Interactive and coordinated visualization approaches for biological data analysis 
 
António Cruz; Joel P Arrais; Penousal Machado
 
 
A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data border= 
 
Zhuo Zhang ; Hao Li; Shuai Jiang; Ruijiang Li; Wanying Li ...
 
 
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions 
 
Damla Senol Cali; Jeremie S Kim; Saugata Ghose ; Can Alkan; Onur Mutlu
 
 
 
Software Review
 
 
 
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes 
 
David Arndt; Ana Marcu; Yongjie Liang ; David S Wishart
 
 
DOOR: a prokaryotic operon database for genome analyses and functional inference 
 
Huansheng Cao; Qin Ma; Xin Chen ; Ying Xu
 
 
Visualizing and comparing circular genomes using the CGView family of tools border= 
 
Paul Stothard ; Jason R Grant; Gary Van Domselaar
 
 
Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data 
 
Shun H Yip; Pak Chung Sham; Junwen Wang
 
 
 
Case Study
 
 
 
Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes 
 
Gaoyang Li; Huansheng Cao; Ying Xu
 
 
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